Running Canu consensus: Broken contigs

[ChloeDG]

I used the following command to create a draft assembly for amplified cDNA from viral RNA

/Linux-amd64/bin/canu -p HBV -d HBV-oxford contigFilter="2 0 1.0 0.5 0" genomeSize=3.2K -nanopore-raw /BC09.fastq

It worked quickly with no errors but the output contigs.fasta is broken into 3 tigs. The consensus.fasta.fai looks like this:

tig00000001_segment0    2527    45  2527    2528
tig00000004_segment0    1762    2618    1762    1763
tig00000005_segment0    1490    4426    1490    1491

I guess this is because it has identified a gap or something, but is there a way to force canu to not break contigs? Let me know if theres anything else you need.

-- Canu snapshot v2.0-development +369 changes (r9862 6cfdadd772614d22446e9c113b8405b489dfe3e5) Linux

[skoren]

I'm not sure this is a gap, since the largest contigs are close to your genome size already and their sum is larger than the genome size. The contigs may just represent variants present in the data but are redundant with each other.

It's also possible you do have gaps. What is the full report from the assembly? Have you mapped the assembly to a reference (assuming you have one)? Have you mapped reads to the reference to see if there are coverage gaps? You could also try the suggestions in #1322 progressively to see if the assembly improves. I also noticed you're using a tip version and not a release, I'd suggest using either the 1.9 or the 2.0 release instead.

[ChloeDG]

I haven't tried mapping it to a reference. We have one that we have made synthetically but it isn't the best. This is the full report: I am trying to make sense of it.

[CORRECTION/READS]
--
-- In sequence store './HBVFL.seqStore':
--   Found 541 reads.
--   Found 640069 bases (200.02 times coverage).
--    
--    G=640069                           sum of  ||               length     num
--    NG         length     index       lengths  ||                range    seqs
--    ----- ------------ --------- ------------  ||  ------------------- -------
--    00010         1452        39        64585  ||       1000-1025           49|-------------------------------------
--    00020         1288        86       128216  ||       1026-1051           46|-----------------------------------
--    00030         1230       137       192272  ||       1052-1077           42|--------------------------------
--    00040         1185       190       256228  ||       1078-1103           28|---------------------
--    00050         1151       245       320435  ||       1104-1129           54|-----------------------------------------
--    00060         1136       301       384432  ||       1130-1155           84|---------------------------------------------------------------
--    00070         1115       358       448640  ||       1156-1181           43|---------------------------------
--    00080         1071       417       512999  ||       1182-1207           34|--------------------------
--    00090         1032       478       577086  ||       1208-1233           29|----------------------
--    00100         1000       540       640069  ||       1234-1259           23|------------------
--    001.000x                 541       640069  ||       1260-1285           21|----------------
--                                               ||       1286-1311           11|---------
--                                               ||       1312-1337           10|--------
--                                               ||       1338-1363            9|-------
--                                               ||       1364-1389            8|------
--                                               ||       1390-1415            5|----
--                                               ||       1416-1441            2|--
--                                               ||       1442-1467            7|------
--                                               ||       1468-1493            5|----
--                                               ||       1494-1519            6|-----
--                                               ||       1520-1545            3|---
--                                               ||       1546-1571            3|---
--                                               ||       1572-1597            1|-
--                                               ||       1598-1623            1|-
--                                               ||       1624-1649            3|---
--                                               ||       1650-1675            4|---
--                                               ||       1676-1701            0|
--                                               ||       1702-1727            3|---
--                                               ||       1728-1753            1|-
--                                               ||       1754-1779            0|
--                                               ||       1780-1805            0|
--                                               ||       1806-1831            4|---
--                                               ||       1832-1857            0|
--                                               ||       1858-1883            1|-
--                                               ||       1884-1909            0|
--                                               ||       1910-1935            0|
--                                               ||       1936-1961            0|
--                                               ||       1962-1987            0|
--                                               ||       1988-2013            0|
--                                               ||       2014-2039            0|
--                                               ||       2040-2065            0|
--                                               ||       2066-2091            0|
--                                               ||       2092-2117            0|
--                                               ||       2118-2143            0|
--                                               ||       2144-2169            0|
--                                               ||       2170-2195            0|
--                                               ||       2196-2221            0|
--                                               ||       2222-2247            0|
--                                               ||       2248-2273            0|
--                                               ||       2274-2299            1|-
--

[CORRECTION/MERS]
--
--  16-mers                                                                                           Fraction
--    Occurrences   NumMers                                                                         Unique Total
--       1-     1         0                                                                        0.0000 0.0000
--       2-     2     22356 ********************************************************************** 0.4739 0.1122
--       3-     4     12504 ***************************************                                0.6521 0.1756
--       5-     7      4721 **************                                                         0.7875 0.2454
--       8-    11      2122 ******                                                                 0.8545 0.2992
--      12-    16      1152 ***                                                                    0.8904 0.3426
--      17-    22       886 **                                                                     0.9119 0.3803
--      23-    29       808 **                                                                     0.9299 0.4236
--      30-    37       571 *                                                                      0.9465 0.4766
--      38-    46       532 *                                                                      0.9577 0.5217
--      47-    56       490 *                                                                      0.9689 0.5789
--      57-    67       353 *                                                                      0.9790 0.6411
--      68-    79       244                                                                        0.9861 0.6937
--      80-    92       118                                                                        0.9911 0.7379
--      93-   106        48                                                                        0.9933 0.7605
--     107-   121        48                                                                        0.9943 0.7726
--     122-   137        18                                                                        0.9953 0.7853
--     138-   154        20                                                                        0.9957 0.7911
--     155-   172        26                                                                        0.9961 0.7993
--     173-   191        42                                                                        0.9967 0.8100
--     192-   211        17                                                                        0.9975 0.8283
--     212-   232        14                                                                        0.9979 0.8369
--     233-   254        16                                                                        0.9982 0.8447
--     255-   277         7                                                                        0.9985 0.8545
--     278-   301         5                                                                        0.9987 0.8593
--     302-   326         3                                                                        0.9988 0.8630
--     327-   352         6                                                                        0.9988 0.8654
--     353-   379         3                                                                        0.9990 0.8707
--     380-   407         2                                                                        0.9990 0.8735
--     408-   436         3                                                                        0.9991 0.8755
--     437-   466         6                                                                        0.9992 0.8799
--     467-   497         0                                                                        0.0000 0.0000
--     498-   529         0                                                                        0.0000 0.0000
--     530-   562         0                                                                        0.0000 0.0000
--     563-   596         1                                                                        0.9993 0.8858
--
--           0 (max occurrences)
--      398395 (total mers, non-unique)
--       47177 (distinct mers, non-unique)
--           0 (unique mers)

[CORRECTION/LAYOUT]
--                             original      original
--                            raw reads     raw reads
--   category                w/overlaps  w/o/overlaps
--   -------------------- ------------- -------------
--   Number of Reads                525          8368
--   Number of Bases             621662         18407
--   Coverage                   194.269         5.752
--   Median                        1143             0
--   Mean                          1184             2
--   N50                           1151          1166
--   Minimum                       1000             0
--   Maximum                       2288          1268
--   
--                                        --------corrected---------  ----------rescued----------
--                             evidence                     expected                     expected
--   category                     reads            raw     corrected            raw     corrected
--   -------------------- -------------  ------------- -------------  ------------- -------------
--   Number of Reads                531             94            94              4             4
--   Number of Bases             628588         132323        128406           4575          4526
--   Coverage                   196.434         41.351        40.127          1.430         1.414
--   Median                        1143           1370          1332           1158          1137
--   Mean                          1183           1407          1366           1143          1131
--   N50                           1151           1385          1350           1173          1157
--   Minimum                       1000           1203          1202           1110          1109
--   Maximum                       2288           1864          1863           1173          1157
--   
--                        --------uncorrected--------
--                                           expected
--   category                       raw     corrected
--   -------------------- ------------- -------------
--   Number of Reads               8795          8795
--   Number of Bases             503171        401102
--   Coverage                   157.241       125.344
--   Median                           0             0
--   Mean                            57            45
--   N50                           1135          1090
--   Minimum                          0             0
--   Maximum                       2288          2271
--   
--   Maximum Memory           546352838

[TRIMMING/READS]
--
-- In sequence store './HBVFL.seqStore':
--   Found 98 reads.
--   Found 122481 bases (38.27 times coverage).
--    
--    G=122481                           sum of  ||               length     num
--    NG         length     index       lengths  ||                range    seqs
--    ----- ------------ --------- ------------  ||  ------------------- -------
--    00010         1553         7        13316  ||        420-447             1|-------
--    00020         1453        15        25118  ||        448-475             0|
--    00030         1366        24        37719  ||        476-503             0|
--    00040         1332        33        49839  ||        504-531             0|
--    00050         1300        42        61662  ||        532-559             0|
--    00060         1256        52        74421  ||        560-587             0|
--    00070         1215        62        86731  ||        588-615             0|
--    00080         1188        72        98710  ||        616-643             2|-------------
--    00090         1136        82       110297  ||        644-671             0|
--    00100          420        97       122481  ||        672-699             1|-------
--    001.000x                  98       122481  ||        700-727             2|-------------
--                                               ||        728-755             0|
--                                               ||        756-783             0|
--                                               ||        784-811             1|-------
--                                               ||        812-839             1|-------
--                                               ||        840-867             3|-------------------
--                                               ||        868-895             0|
--                                               ||        896-923             0|
--                                               ||        924-951             1|-------
--                                               ||        952-979             0|
--                                               ||        980-1007            0|
--                                               ||       1008-1035            0|
--                                               ||       1036-1063            1|-------
--                                               ||       1064-1091            1|-------
--                                               ||       1092-1119            0|
--                                               ||       1120-1147            5|--------------------------------
--                                               ||       1148-1175            3|-------------------
--                                               ||       1176-1203           10|---------------------------------------------------------------
--                                               ||       1204-1231            8|---------------------------------------------------
--                                               ||       1232-1259            7|---------------------------------------------
--                                               ||       1260-1287            4|--------------------------
--                                               ||       1288-1315            9|---------------------------------------------------------
--                                               ||       1316-1343            7|---------------------------------------------
--                                               ||       1344-1371            8|---------------------------------------------------
--                                               ||       1372-1399            3|-------------------
--                                               ||       1400-1427            3|-------------------
--                                               ||       1428-1455            2|-------------
--                                               ||       1456-1483            5|--------------------------------
--                                               ||       1484-1511            1|-------
--                                               ||       1512-1539            1|-------
--                                               ||       1540-1567            1|-------
--                                               ||       1568-1595            0|
--                                               ||       1596-1623            2|-------------
--                                               ||       1624-1651            1|-------
--                                               ||       1652-1679            1|-------
--                                               ||       1680-1707            0|
--                                               ||       1708-1735            2|-------------
--                                               ||       1736-1763            0|
--                                               ||       1764-1791            0|
--                                               ||       1792-1819            1|-------
--

[TRIMMING/MERS]
--
--  22-mers                                                                                           Fraction
--    Occurrences   NumMers                                                                         Unique Total
--       1-     1         0                                                                        0.0000 0.0000
--       2-     2      1974 ********************************************************************** 0.3279 0.0389
--       3-     4       767 ***************************                                            0.3963 0.0511
--       5-     7       504 *****************                                                      0.4924 0.0761
--       8-    11       565 ********************                                                   0.5678 0.1078
--      12-    16      1212 ******************************************                             0.6572 0.1644
--      17-    22       655 ***********************                                                0.8612 0.3434
--      23-    29        79 **                                                                     0.9464 0.4395
--      30-    37        78 **                                                                     0.9575 0.4571
--      38-    46        36 *                                                                      0.9696 0.4813
--      47-    56        23                                                                        0.9754 0.4961
--      57-    67        13                                                                        0.9789 0.5069
--      68-    79         7                                                                        0.9811 0.5151
--      80-    92        11                                                                        0.9824 0.5211
--      93-   106         0                                                                        0.0000 0.0000
--     107-   121         4                                                                        0.9841 0.5297
--     122-   137         2                                                                        0.9847 0.5345
--     138-   154        15                                                                        0.9852 0.5385
--     155-   172        16                                                                        0.9875 0.5588
--     173-   191         3                                                                        0.9902 0.5848
--     192-   211         4                                                                        0.9909 0.5923
--     212-   232         1                                                                        0.9914 0.5986
--     233-   254        12                                                                        0.9915 0.6009
--     255-   277         0                                                                        0.0000 0.0000
--     278-   301         1                                                                        0.9935 0.6302
--     302-   326         0                                                                        0.0000 0.0000
--     327-   352         1                                                                        0.9937 0.6337
--     353-   379         1                                                                        0.9939 0.6372
--     380-   407         0                                                                        0.0000 0.0000
--     408-   436         0                                                                        0.0000 0.0000
--     437-   466         0                                                                        0.0000 0.0000
--     467-   497         0                                                                        0.0000 0.0000
--     498-   529         2                                                                        0.9940 0.6424
--     530-   562         1                                                                        0.9944 0.6530
--     563-   596        10                                                                        0.9945 0.6587
--     597-   631         4                                                                        0.9962 0.7164
--
--           0 (max occurrences)
--      101440 (total mers, non-unique)
--        6021 (distinct mers, non-unique)
--           0 (unique mers)

[TRIMMING/TRIMMING]
--  PARAMETERS:
--  ----------
--     1000    (reads trimmed below this many bases are deleted)
--   0.1200    (use overlaps at or below this fraction error)
--      500    (break region if overlap is less than this long, for 'largest covered' algorithm)
--        2    (break region if overlap coverage is less than this many reads, for 'largest covered' algorithm)
--  
--  INPUT READS:
--  -----------
--    8893 reads       122481 bases (reads processed)
--       0 reads            0 bases (reads not processed, previously deleted)
--       0 reads            0 bases (reads not processed, in a library where trimming isn't allowed)
--  
--  OUTPUT READS:
--  ------------
--      63 reads        76371 bases (trimmed reads output)
--       0 reads            0 bases (reads with no change, kept as is)
--    8801 reads         4579 bases (reads with no overlaps, deleted)
--      29 reads        34770 bases (reads with short trimmed length, deleted)
--  
--  TRIMMING DETAILS:
--  ----------------
--      50 reads         3231 bases (bases trimmed from the 5' end of a read)
--      55 reads         3530 bases (bases trimmed from the 3' end of a read)

[TRIMMING/SPLITTING]
--  PARAMETERS:
--  ----------
--     1000    (reads trimmed below this many bases are deleted)
--   0.1200    (use overlaps at or below this fraction error)
--  INPUT READS:
--  -----------
--      63 reads        83132 bases (reads processed)
--    8830 reads        39349 bases (reads not processed, previously deleted)
--       0 reads            0 bases (reads not processed, in a library where trimming isn't allowed)
--  
--  PROCESSED:
--  --------
--       0 reads            0 bases (no overlaps)
--       0 reads            0 bases (no coverage after adjusting for trimming done already)
--       0 reads            0 bases (processed for chimera)
--       0 reads            0 bases (processed for spur)
--      63 reads        83132 bases (processed for subreads)
--  
--  READS WITH SIGNALS:
--  ------------------
--       0 reads            0 signals (number of 5' spur signal)
--       0 reads            0 signals (number of 3' spur signal)
--       0 reads            0 signals (number of chimera signal)
--       0 reads            0 signals (number of subread signal)
--  
--  SIGNALS:
--  -------
--       0 reads            0 bases (size of 5' spur signal)
--       0 reads            0 bases (size of 3' spur signal)
--       0 reads            0 bases (size of chimera signal)
--       0 reads            0 bases (size of subread signal)
--  
--  TRIMMING:
--  --------
--       0 reads            0 bases (trimmed from the 5' end of the read)
--       0 reads            0 bases (trimmed from the 3' end of the read)

[UNITIGGING/READS]
--
-- In sequence store './HBVFL.seqStore':
--   Found 63 reads.
--   Found 76371 bases (23.86 times coverage).
--    
--    G=76371                            sum of  ||               length     num
--    NG         length     index       lengths  ||                range    seqs
--    ----- ------------ --------- ------------  ||  ------------------- -------
--    00010         1467         4         7666  ||       1009-1023            2|---------------------
--    00020         1335        10        15919  ||       1024-1038            0|
--    00030         1257        16        23663  ||       1039-1053            2|---------------------
--    00040         1235        22        31130  ||       1054-1068            4|------------------------------------------
--    00050         1196        28        38422  ||       1069-1083            2|---------------------
--    00060         1162        35        46649  ||       1084-1098            1|-----------
--    00070         1136        41        53540  ||       1099-1113            2|---------------------
--    00080         1119        48        61440  ||       1114-1128            4|------------------------------------------
--    00090         1066        55        69065  ||       1129-1143            6|---------------------------------------------------------------
--    00100         1009        62        76371  ||       1144-1158            4|------------------------------------------
--    001.000x                  63        76371  ||       1159-1173            2|---------------------
--                                               ||       1174-1188            5|-----------------------------------------------------
--                                               ||       1189-1203            2|---------------------
--                                               ||       1204-1218            0|
--                                               ||       1219-1233            4|------------------------------------------
--                                               ||       1234-1248            4|------------------------------------------
--                                               ||       1249-1263            3|--------------------------------
--                                               ||       1264-1278            1|-----------
--                                               ||       1279-1293            1|-----------
--                                               ||       1294-1308            1|-----------
--                                               ||       1309-1323            1|-----------
--                                               ||       1324-1338            2|---------------------
--                                               ||       1339-1353            2|---------------------
--                                               ||       1354-1368            1|-----------
--                                               ||       1369-1383            0|
--                                               ||       1384-1398            0|
--                                               ||       1399-1413            0|
--                                               ||       1414-1428            1|-----------
--                                               ||       1429-1443            1|-----------
--                                               ||       1444-1458            0|
--                                               ||       1459-1473            2|---------------------
--                                               ||       1474-1488            0|
--                                               ||       1489-1503            1|-----------
--                                               ||       1504-1518            1|-----------
--                                               ||       1519-1533            0|
--                                               ||       1534-1548            0|
--                                               ||       1549-1563            0|
--                                               ||       1564-1578            0|
--                                               ||       1579-1593            0|
--                                               ||       1594-1608            0|
--                                               ||       1609-1623            0|
--                                               ||       1624-1638            0|
--                                               ||       1639-1653            0|
--                                               ||       1654-1668            0|
--                                               ||       1669-1683            0|
--                                               ||       1684-1698            0|
--                                               ||       1699-1713            0|
--                                               ||       1714-1728            1|-----------
--

[UNITIGGING/MERS]
--
--  22-mers                                                                                           Fraction
--    Occurrences   NumMers                                                                         Unique Total
--       1-     1         0                                                                        0.0000 0.0000
--       2-     2       680 ***************************************                                0.1673 0.0196
--       3-     4       435 *************************                                              0.2158 0.0281
--       5-     7       442 *************************                                              0.3214 0.0556
--       8-    11       532 ******************************                                         0.4171 0.0947
--      12-    16      1209 ********************************************************************** 0.5477 0.1762
--      17-    22       599 **********************************                                     0.8492 0.4360
--      23-    29        46 **                                                                     0.9604 0.5583
--      30-    37         9                                                                        0.9705 0.5739
--      38-    46         6                                                                        0.9729 0.5789
--      47-    56        10                                                                        0.9749 0.5844
--      57-    67         0                                                                        0.0000 0.0000
--      68-    79         9                                                                        0.9766 0.5898
--      80-    92        20 *                                                                      0.9793 0.6018
--      93-   106        12                                                                        0.9840 0.6257
--     107-   121         2                                                                        0.9867 0.6414
--     122-   137        14                                                                        0.9872 0.6449
--     138-   154         0                                                                        0.0000 0.0000
--     155-   172         0                                                                        0.0000 0.0000
--     173-   191         0                                                                        0.0000 0.0000
--     192-   211         0                                                                        0.0000 0.0000
--     212-   232         0                                                                        0.0000 0.0000
--     233-   254         1                                                                        0.9906 0.6725
--     255-   277         1                                                                        0.9909 0.6762
--     278-   301         0                                                                        0.0000 0.0000
--     302-   326         0                                                                        0.0000 0.0000
--     327-   352         0                                                                        0.0000 0.0000
--     353-   379         2                                                                        0.9911 0.6813
--     380-   407         5                                                                        0.9919 0.6977
--     408-   436        10                                                                        0.9929 0.7210
--     437-   466         0                                                                        0.0000 0.0000
--     467-   497         0                                                                        0.0000 0.0000
--     498-   529         0                                                                        0.0000 0.0000
--     530-   562         0                                                                        0.0000 0.0000
--     563-   596         0                                                                        0.0000 0.0000
--     597-   631         0                                                                        0.0000 0.0000
--     632-   667         0                                                                        0.0000 0.0000
--     668-   704         2                                                                        0.9953 0.7839
--     705-   742         1                                                                        0.9958 0.8042
--     743-   781         1                                                                        0.9961 0.8154
--     782-   821        15                                                                        0.9963 0.8267
--
--           0 (max occurrences)
--       69347 (total mers, non-unique)
--        4064 (distinct mers, non-unique)
--           0 (unique mers)

[UNITIGGING/OVERLAPS]
--   category            reads     %          read length        feature size or coverage  analysis
--   ----------------  -------  -------  ----------------------  ------------------------  --------------------
--   middle-missing          0    0.00        0.00 +- 0.00             0.00 +- 0.00       (bad trimming)
--   middle-hump             1    0.18     1240.00 +- 0.00            13.00 +- 0.00       (bad trimming)
--   no-5-prime              1    0.18     1468.00 +- 0.00             1.00 +- 0.00       (bad trimming)
--   no-3-prime              1    0.18     1281.00 +- 0.00             4.00 +- 0.00       (bad trimming)
--   
--   low-coverage            0    0.00        0.00 +- 0.00             0.00 +- 0.00       (easy to assemble, potential for lower quality consensus)
--   unique                 25    4.62     1151.08 +- 84.37           17.39 +- 4.14       (easy to assemble, perfect, yay)
--   repeat-cont             0    0.00        0.00 +- 0.00             0.00 +- 0.00       (potential for consensus errors, no impact on assembly)
--   repeat-dove             0    0.00        0.00 +- 0.00             0.00 +- 0.00       (hard to assemble, likely won't assemble correctly or even at all)
--   
--   span-repeat             7    1.29     1246.71 +- 137.12         881.29 +- 463.05     (read spans a large repeat, usually easy to assemble)
--   uniq-repeat-cont       20    3.70     1188.75 +- 100.27                              (should be uniquely placed, low potential for consensus errors, no impact on assembly)
--   uniq-repeat-dove        8    1.48     1387.88 +- 195.74                              (will end contigs, potential to misassemble)
--   uniq-anchor             0    0.00        0.00 +- 0.00             0.00 +- 0.00       (repeat read, with unique section, probable bad read)

[UNITIGGING/ADJUSTMENT]
-- No report available.

[UNITIGGING/CONTIGS]
-- Found, in version 1, after unitig construction:
--   contigs:      2 sequences, total length 3961 bp (including 0 repeats of total length 0 bp).
--   bubbles:      1 sequences, total length 1799 bp.
--   unassembled:  19 sequences, total length 22971 bp.
--
-- Contig sizes based on genome size 3.2kbp:
--
--            NG (bp)  LG (contigs)    sum (bp)
--         ----------  ------------  ----------
--     10        2439             1        2439
--     20        2439             1        2439
--     30        2439             1        2439
--     40        2439             1        2439
--     50        2439             1        2439
--     60        2439             1        2439
--     70        2439             1        2439
--     80        1522             2        3961
--     90        1522             2        3961
--    100        1522             2        3961
--    110        1522             2        3961
--    120        1522             2        3961
--

[UNITIGGING/CONSENSUS]
-- Found, in version 2, after consensus generation:
--   contigs:      2 sequences, total length 3983 bp (including 0 repeats of total length 0 bp).
--   bubbles:      1 sequences, total length 1770 bp.
--   unassembled:  19 sequences, total length 22971 bp.
--
-- Contig sizes based on genome size 3.2kbp:
--
--            NG (bp)  LG (contigs)    sum (bp)
--         ----------  ------------  ----------
--     10        2499             1        2499
--     20        2499             1        2499
--     30        2499             1        2499
--     40        2499             1        2499
--     50        2499             1        2499
--     60        2499             1        2499
--     70        2499             1        2499
--     80        1484             2        3983
--     90        1484             2        3983
--    100        1484             2        3983
--    110        1484             2        3983
--    120        1484             2        3983
--

Is there something in the report that speaks to you about what it could be? I will try the suggestions in the previous post in the mean time:-) Thank you.

[ChloeDG]

I have a few naive questions trying to understand the report. Perhaps you have a link/ read.me that answers these somewhere, but I couldn't locate it (sorry).

• What is meant by bubbles?
• My report is saying that I have 2 contigs and 1 bubble. You say that it is likely that the contigs are redundant with each other. Does that mean that half of my reads will align to each contig? Are there some stats in the report that show how many reads will align to each that I am missing?

Thank you.

[skoren]

Have you tried running the alternate parameter assemblies?

Bubbles are things contained in a contig, so the bubble is definitely redundant. By redundant, I meant the contigs may have similarity to each other and are assembling the same sequence. The *.contigs.layout.tigInfo will give you stats on how many reads are in each contig and their coverage while *contigs.layout.readToTig will tell you the position of every read in the assembly.

[ChloeDG]

Thank you so much. Do you mean the suggested parameters in #1322? I will try them now.

[ChloeDG]

After playing with different parameters and mapping the tigs to a reference we made I am happy that Canu has assembled my genome well. Thanks for your help!