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broadinstitute
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pilon
Pilon is an automated genome assembly improvement and variant detection tool
GNU General Public License v2.0
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Inappropriate call if not paired read?? what??
#73
zapataf
closed
5 years ago
1
Pilon running error
#72
Jung19911124
closed
5 years ago
1
Erroneous expansion of repeats?
#71
EarlyEvol
closed
6 years ago
2
Is it necessary to mark/remove duplicates before using pilon?
#70
zengxiaofei
closed
5 years ago
1
Fix Ambiguous Bases - finding, possibly fixing, but not writing changes
#69
Roli-Wilhelm
closed
5 years ago
4
Chimeric sequences
#68
faraz89
closed
5 years ago
2
advice for finishing a pacbio sequel yeast genome asm
#67
splaisan
closed
5 years ago
0
pilon will call snpindel in repeat region of ref sequence ?
#66
orangeSi
closed
5 years ago
0
Exception in thread "main" java.lang.reflect.InvocationTargetException
#65
wenjiexiaomeng
closed
5 years ago
1
Multiple rounds of polishing using pilon
#64
efratca
closed
5 years ago
1
Coverage is always 0
#63
CVan19
closed
5 years ago
3
GATK Indel Realigner
#62
ArashBayat
closed
5 years ago
1
Caused by: java.lang.IllegalArgumentException: Cannot add sequence that already exists in SAMSequenceDictionary:
#61
tiramisutes
closed
5 years ago
1
using 250bp paired reads in pilon (which the reads of a pair may overlap each other)
#60
dgordon562
closed
5 years ago
1
[Question] Impact of kmer size (--K) in correction
#59
ghost
closed
5 years ago
1
Pilon with MP + PE cuses too many cpus and memory
#58
jaworskicoline
closed
5 years ago
1
use pilon to polish cause error
#57
lijingjing1
closed
5 years ago
1
Dovetail data for Pilon
#56
dcopetti
closed
5 years ago
1
pilon on sge cluster
#55
dcopetti
closed
5 years ago
1
Crash correcting single contig
#54
TomHarrop
closed
5 years ago
2
Enquiry for pilon running virtual memory
#53
zx0223winner
closed
7 years ago
2
Pilon running commands enquiry
#52
zx0223winner
closed
7 years ago
0
Inappropriate call if not paired read?
#51
jordur
opened
7 years ago
4
Using pilon with RNAseq data
#50
suryasaha
closed
7 years ago
3
Can pilon work with an assembly with ambiguous bases?
#49
caonetto
closed
7 years ago
1
VCF output exception "Can't fetch base outside region"
#48
pd3
closed
5 years ago
3
chunk the genome in Pilon
#47
bostanict
closed
7 years ago
1
dies with Invalid reference index -1
#46
dcopetti
closed
5 years ago
3
Predef.scala:224
#45
diaparim
closed
7 years ago
1
Issue running pilon : java.lang.OutOfMemoryError: Java heap space
#44
RxLoutre
closed
7 years ago
10
Generating FastQ of assembly from Pilon output
#43
dbrowneup
closed
7 years ago
1
Very old version of htsjdk.jar
#42
tseemann
closed
7 years ago
1
BWA only marks FR reads as proper when mapping mate pairs
#41
melop
closed
7 years ago
1
Question: Range of indels sizes that are corrected by Pilon
#40
chad388
closed
7 years ago
2
Question re: uncorrected ONP errors using Pilon
#39
cjfields
closed
7 years ago
3
BED Co-ordinates Off-by-1 bug
#38
nathanhaigh
closed
7 years ago
1
pilon runtime
#37
madhubioinfo
closed
7 years ago
1
Pilon crashing due to NegativeArraySizeException
#36
ctxchris
closed
7 years ago
4
pilon fails to correct hetozygous indel errors
#35
dgordon562
closed
7 years ago
7
[Question] PacBio reads and Pilon
#34
RxLoutre
closed
7 years ago
0
Unknown Exception
#33
kevlim83
closed
7 years ago
1
Crash due to GC overhead limit exceed
#32
gucascau
closed
7 years ago
10
Clean metagenomics contigs
#31
davidvilanova
closed
7 years ago
2
switches to regex to better identify targets with start and stop
#30
bwlang
closed
7 years ago
1
Cannot handle : in contig names when using --targets
#29
bwlang
closed
7 years ago
0
fix breaks should introduce new gaps only on majority
#28
tolot27
closed
7 years ago
1
pilon gives different results--does it have any randomness?
#27
dgordon562
closed
7 years ago
1
Pilon OutOfMemoryError
#26
lijingjing1
closed
7 years ago
6
number of threads
#25
JahnDavik
closed
7 years ago
1
negative genome size
#24
bwlang
closed
7 years ago
1
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