Remaining discrepancies `A primer on anvi'o`

[raissameyer]

Collection of discrepancies I noticed between the tutorial (after Mete's updates) and my outputs. I'll write one comment per issue as I notice them.

[raissameyer]

Inferring taxonomy for metagenomes

[!NOTE] The names in the output of the following two commands is not the same as on the tutorial page Ribosomal_S6_2915 (Tutorial) Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_11655 (my output).

command

anvi-estimate-scg-taxonomy -c CONTIGS.db \
                           --metagenome-mode```

output

+----------------------------------------------------------+--------------------+---------------------------------------------------------------------------------------------------------------------------------+
|                                                          |   percent_identity | taxonomy                                                                                                                        |
+==========================================================+====================+=================================================================================================================================+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_11655 |               98.9 | Bacteria / Firmicutes / Bacilli / Staphylococcales / Staphylococcaceae / Staphylococcus / Staphylococcus epidermidis            |
+----------------------------------------------------------+--------------------+---------------------------------------------------------------------------------------------------------------------------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_12163 |               98.9 | Bacteria / Firmicutes / Bacilli / Staphylococcales / Staphylococcaceae / Staphylococcus / Staphylococcus hominis                |
+----------------------------------------------------------+--------------------+---------------------------------------------------------------------------------------------------------------------------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_15200 |               98.9 | Bacteria / Firmicutes / Bacilli / Lactobacillales / Lactobacillaceae / Leuconostoc / Leuconostoc citreum                        |
+----------------------------------------------------------+--------------------+---------------------------------------------------------------------------------------------------------------------------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_25880 |               98.9 | Bacteria / Firmicutes / Clostridia / Tissierellales / Peptoniphilaceae / Finegoldia /                                           |
+----------------------------------------------------------+--------------------+---------------------------------------------------------------------------------------------------------------------------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_2915  |               97.9 | Bacteria / Firmicutes / Bacilli / Lactobacillales / Enterococcaceae / Enterococcus / Enterococcus faecalis                      |
+----------------------------------------------------------+--------------------+---------------------------------------------------------------------------------------------------------------------------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_29818 |               97.9 | Bacteria / Firmicutes / Bacilli / Lactobacillales / Streptococcaceae / Streptococcus /                                          |
+----------------------------------------------------------+--------------------+---------------------------------------------------------------------------------------------------------------------------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_30904 |               98.1 | Bacteria / Firmicutes / Clostridia / Tissierellales / Peptoniphilaceae / Anaerococcus / Anaerococcus nagyae                     |
+----------------------------------------------------------+--------------------+---------------------------------------------------------------------------------------------------------------------------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_4484  |               98.9 | Bacteria / Firmicutes / Clostridia / Tissierellales / Peptoniphilaceae / Peptoniphilus / Peptoniphilus lacydonensis             |
+----------------------------------------------------------+--------------------+---------------------------------------------------------------------------------------------------------------------------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_6421  |                100 | Bacteria / Actinobacteriota / Actinomycetia / Propionibacteriales / Propionibacteriaceae / Cutibacterium / Cutibacterium avidum |
+----------------------------------------------------------+--------------------+---------------------------------------------------------------------------------------------------------------------------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_7660  |               98.9 | Bacteria / Firmicutes / Bacilli / Staphylococcales / Staphylococcaceae / Staphylococcus /                                       |
+----------------------------------------------------------+--------------------+---------------------------------------------------------------------------------------------------------------------------------+

command

anvi-estimate-scg-taxonomy -c CONTIGS.db \
>                            -p PROFILE.db \
>                            --metagenome-mode \
>                            --compute-scg-coverages

output

+----------------------------------------------------------+--------------------+--------------------------------+-----------+-----------+----------+-----------+-----------+--------------+
|                                                          |   percent_identity | taxonomy                       |   DAY_15A |   DAY_15B |   DAY_16 |   DAY_17A |   DAY_17B | ... 6 more   |
+==========================================================+====================+================================+===========+===========+==========+===========+===========+==============+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_2915  |               97.9 | (s) Enterococcus faecalis      |   372.512 |   699.853 |  663.241 |    186.34 |    1149.6 | ... 6 more   |
+----------------------------------------------------------+--------------------+--------------------------------+-----------+-----------+----------+-----------+-----------+--------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_11655 |               98.9 | (s) Staphylococcus epidermidis |   112.694 |   172.478 |  147.304 |   23.3901 |   140.769 | ... 6 more   |
+----------------------------------------------------------+--------------------+--------------------------------+-----------+-----------+----------+-----------+-----------+--------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_4484  |               98.9 | (s) Peptoniphilus lacydonensis |         0 |         0 |        0 |         0 |         0 | ... 6 more   |
+----------------------------------------------------------+--------------------+--------------------------------+-----------+-----------+----------+-----------+-----------+--------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_7660  |               98.9 | (g) Staphylococcus             |         0 |         0 |        0 |         0 |         0 | ... 6 more   |
+----------------------------------------------------------+--------------------+--------------------------------+-----------+-----------+----------+-----------+-----------+--------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_6421  |                100 | (s) Cutibacterium avidum       |   17.8935 |   5.87368 |  4.79909 |         0 |         0 | ... 6 more   |
+----------------------------------------------------------+--------------------+--------------------------------+-----------+-----------+----------+-----------+-----------+--------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_12163 |               98.9 | (s) Staphylococcus hominis     |   2.39322 |   22.5447 |  13.2806 |         0 |   9.94853 | ... 6 more   |
+----------------------------------------------------------+--------------------+--------------------------------+-----------+-----------+----------+-----------+-----------+--------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_15200 |               98.9 | (s) Leuconostoc citreum        |         0 |         0 |  1.86532 |         0 |    1.6936 | ... 6 more   |
+----------------------------------------------------------+--------------------+--------------------------------+-----------+-----------+----------+-----------+-----------+--------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_29818 |               97.9 | (g) Streptococcus              |         0 |         0 |        0 |         0 |         0 | ... 6 more   |
+----------------------------------------------------------+--------------------+--------------------------------+-----------+-----------+----------+-----------+-----------+--------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_25880 |               98.9 | (g) Finegoldia                 |         0 |         0 |        0 |         0 |         0 | ... 6 more   |
+----------------------------------------------------------+--------------------+--------------------------------+-----------+-----------+----------+-----------+-----------+--------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_30904 |               98.1 | (s) Anaerococcus nagyae        |  0.528958 |         0 |  0.14157 |         0 |         0 | ... 6 more   |
+----------------------------------------------------------+--------------------+--------------------------------+-----------+-----------+----------+-----------+-----------+--------------+

[raissameyer]

Manual identification of genomes in the Infant Gut Dataset

[!NOTE] For the manual identification of bins it would be helpful for the screenshot to include the information in the Bins tab (Len, Comp., Red.)

Image from tutorial

Image from my interface (please disregard that the bins I assigned are slightly different from the tutorial)

[raissameyer]

Chapter II: Automatic Binning

Manually curating automatic binning outputs

[!NOTE] Minor note, but I got a slightly different redundancy value than you report in the text (maxbin_007 has a redundancy value of 22% in the tutorial, 18.31% for me)

Text in tutorial

It is clear that some bins are not as well-resolved as others. For instance, bins maxbin_007 and maxbin_008 have redundancy estimates of 22% and 91%, respectively, which suggests each of them describe multiple distinct populations. Well, clearly we would have preferred those bins to behave.

command

anvi-estimate-genome-completeness -p PROFILE.db \
                                   -c CONTIGS.db \
                                   -C MAXBIN

my output

Bins in collection "MAXBIN"
===============================================
+------------+----------+--------------+----------------+----------------+--------------+----------------+                            
| bin name   | domain   |   confidence |   % completion |   % redundancy |   num_splits |   total length |
+============+==========+==============+================+================+==============+================+
| maxbin_001 | BACTERIA |            1 |            100 |           4.23 |          148 |        2969341 |
+------------+----------+--------------+----------------+----------------+--------------+----------------+
| maxbin_002 | BACTERIA |            1 |          94.37 |              0 |           88 |        1801068 |
+------------+----------+--------------+----------------+----------------+--------------+----------------+
| maxbin_003 | BACTERIA |          0.7 |          81.69 |           2.82 |          144 |        2764617 |
+------------+----------+--------------+----------------+----------------+--------------+----------------+
| maxbin_004 | BACTERIA |            1 |          97.18 |           1.41 |          188 |        2571878 |
+------------+----------+--------------+----------------+----------------+--------------+----------------+
| maxbin_005 | BACTERIA |            1 |          98.59 |              0 |          151 |        2555414 |
+------------+----------+--------------+----------------+----------------+--------------+----------------+
| maxbin_006 | BACTERIA |          0.7 |          78.87 |           5.63 |          305 |        2901149 |
+------------+----------+--------------+----------------+----------------+--------------+----------------+
| maxbin_007 | BACTERIA |          0.4 |          54.93 |          18.31 |          724 |        3230717 |
+------------+----------+--------------+----------------+----------------+--------------+----------------+
| maxbin_008 | BACTERIA |          0.8 |          87.32 |          90.14 |         1657 |        3056818 |
+------------+----------+--------------+----------------+----------------+--------------+----------------+
| maxbin_009 | EUKARYA  |          0.8 |          83.13 |           7.23 |         1379 |       13915165 |
+------------+----------+--------------+----------------+----------------+--------------+----------------+

[ivagljiva]

Thanks for the heads up on these issues @raissameyer :) I started a branch (IGT_fixes_from_Raissa) and fixed the table outputs. I didn't want to update the binning screenshot myself since it has nice colors, so I leave that one to @metehaansever :)