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jdidion
/
atropos
An NGS read trimming tool that is specific, sensitive, and speedy. (production)
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Segmentation Fault After Closing SequenceReader
#88
jessrosenfield
closed
4 years ago
7
atropos does not work with python 3.8 because of clock module
#87
kingralph80
closed
4 years ago
2
Error when using BAM file as input
#86
llvisser
closed
4 years ago
10
atropos detect output
#85
nservant
closed
4 years ago
1
Question about adapter removal and length filtering
#84
ElDeveloper
closed
4 years ago
2
Replace pysam with bamnostic
#83
jdidion
closed
4 years ago
1
Add option to overwrite reads with nextseq low quality
#82
jessrosenfield
opened
5 years ago
1
Atropos does not output read 2 fastq provided by `-p` argument in paired end mode
#81
jessrosenfield
closed
5 years ago
2
IndexError: list index out of range
#80
aistBMRG
closed
5 years ago
2
-i example should use negative value to trim end of read
#79
yangruialex
closed
5 years ago
1
gzip error code -9, different than issue #62?
#78
pkMyt1
opened
5 years ago
2
trim nextera adapters
#77
lmanchon
closed
5 years ago
3
Typo
#76
frederic-mahe
closed
5 years ago
0
option to support -a "ADAPTER;max_error_rate=0.2;min_overlap=5"
#75
MarinusVL
opened
5 years ago
0
Add option to configure pysam options when reading SAM/BAM file.
#74
okartal
closed
5 years ago
6
report ouput file is overwritten
#73
frederic-mahe
closed
5 years ago
13
correction to fix for #64
#72
gmagoon
closed
4 years ago
1
Trimming fails
#71
parkerac
closed
4 years ago
16
How to interpret output from detect function
#70
parkerac
closed
5 years ago
3
Initial Update
#69
pyup-bot
closed
6 years ago
0
Encountering assertion error when using --error-rate and --insert-match-error-rate
#68
countdigi
closed
6 years ago
4
Auto trim feature
#67
wckdouglas
closed
6 years ago
1
Support UMIs from a third input file
#66
chapmanb
closed
4 years ago
3
Detect adapters from overhangs of aligned inserts.
#65
jdidion
opened
6 years ago
0
Adapter removal with wildcard N bases behaves unexpectedly with insert alignment
#64
gmagoon
closed
6 years ago
5
adding feature for extracting UMIs (issue #61)
#63
wckdouglas
closed
6 years ago
3
Add option to disable use of system gzip
#62
gmagoon
opened
6 years ago
3
Support UMI extraction
#61
jdidion
closed
4 years ago
5
Add "auto" mode for paired-end adapter trimming
#60
jdidion
closed
4 years ago
3
atropos bioconda version 1.1.16
#59
cokelaer
closed
6 years ago
3
--nextseq-trim should trim from both reads when paired reads are given
#58
pkMyt1
closed
6 years ago
1
legacy_report stops as soon as an adapter sequence is not trimmed
#57
cokelaer
closed
6 years ago
2
Typo
#56
frederic-mahe
closed
6 years ago
0
Trimming Thruplex adapters
#55
pkMyt1
opened
6 years ago
0
No module named lzma
#54
pkMyt1
closed
6 years ago
4
Config file vs cli for parameters
#53
pkMyt1
opened
6 years ago
1
art-skewer docker is broken (both in dockerhub and dockerfile)
#52
antonkulaga
closed
6 years ago
1
Error correction is sometimes not performed on reads of unequal length.
#51
jdidion
closed
6 years ago
1
RFE: SImilar options to trimmomatic's CROP
#50
lbeltrame
opened
6 years ago
4
Fix parameter for quality trimming
#49
ghost
closed
6 years ago
0
base1 = r1_seq[i] IndexError: list index out of range
#48
antonkulaga
closed
6 years ago
2
OverflowError: int too large to convert to float
#47
antonkulaga
closed
6 years ago
6
minor discrepancy between cutadapt and atropos report
#46
cokelaer
closed
6 years ago
1
Fix missing hyphen in "--aligner insert"
#45
ghost
closed
6 years ago
0
Silent failure when specifying adapter files without the 'file:' prefix
#44
jdidion
closed
6 years ago
1
Errors with NULL FASTQ sequences
#43
timp0
closed
6 years ago
3
discrepancy in reports between cutadapt and atropos on the "expect" column
#42
cokelaer
closed
6 years ago
1
progress bar error
#41
cokelaer
closed
6 years ago
4
gzipped file created by atropos cannot be parsed by pysam.
#40
cokelaer
closed
6 years ago
9
miRNA option Error
#39
mottodora
closed
6 years ago
2
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