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jdidion
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atropos
An NGS read trimming tool that is specific, sensitive, and speedy. (production)
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Parallelized atropos trim produces MulticoreError
#38
cshenanigans
closed
6 years ago
5
Error with long reads
#37
dleopold
closed
6 years ago
5
Progress bars don't increment correctly when batch size > 1 used
#36
jdidion
closed
7 years ago
1
Known adapter detector not detecting known adapters
#35
jdidion
closed
7 years ago
1
Error when using --sra with json output
#34
jdidion
closed
7 years ago
0
Propagate header when input and output files are both SAM/BAM format
#33
jdidion
closed
4 years ago
0
SAM output does not contain header
#32
jdidion
closed
7 years ago
1
ERROR: Unknown error
#31
joonlee3
closed
6 years ago
4
Error atropos trim using multiple threads
#30
ekopylova
closed
7 years ago
2
Atropos uses legacy mode when paired-end quality/N-trimming is performed without also adapter-trimming
#29
jdidion
closed
7 years ago
1
feature idea: adapters by platform name
#28
antonkulaga
closed
6 years ago
2
Allow a config file to supplement command line options
#27
jdidion
closed
7 years ago
3
Detect command should determine whether adapters are 5' or 3'
#26
jdidion
opened
7 years ago
9
Improve heuristic detection for short reads
#25
jdidion
opened
7 years ago
1
Improve documentation on known adapters file
#24
jdidion
opened
7 years ago
0
Progress bar counts batches rather than reads
#23
jdidion
closed
6 years ago
1
atropos does not seem to cut most of adapters and primers
#22
antonkulaga
closed
7 years ago
13
UnboundLocalError: local variable 'name3' referenced before assignment
#21
antonkulaga
closed
7 years ago
1
antropos detect output as fasta
#20
antonkulaga
closed
7 years ago
2
for many files I get atropos.io.seqio.FormatError: FASTQ file ended prematurely
#19
antonkulaga
closed
7 years ago
5
bash support to make it cromwell-friendly
#18
antonkulaga
closed
7 years ago
0
single read adapter detection does not work
#17
antonkulaga
closed
7 years ago
1
How to specify multiple adapters?
#16
endrebak
closed
7 years ago
1
Wrong Travis CI badge at PyPI
#15
vmikk
closed
7 years ago
1
Error with `detect` adapters
#14
vmikk
closed
7 years ago
4
changes in log
#13
cokelaer
closed
7 years ago
6
atropos version 1.1.2 on conda hangs while pip version works
#12
cokelaer
closed
7 years ago
2
conda install: requirements incompatible for 3+
#11
endrebak
closed
7 years ago
2
pip install fails on py3.6
#10
endrebak
closed
7 years ago
3
Merge the reorg branch with master
#9
jdidion
closed
7 years ago
1
InsertAligner adds wrong number of N's when masking adapters
#8
jdidion
closed
7 years ago
1
Update modifiers.py
#7
llllaaaa
closed
7 years ago
2
Automatically detect adapter sequences during trim
#6
jdidion
opened
7 years ago
11
Add nanopore-specific options
#5
jdidion
opened
7 years ago
0
Atropos can hang in multi-threaded mode due to insufficient memory
#4
jdidion
closed
6 years ago
1
ShadowRegression error estimation is incredibly slow
#3
jdidion
closed
6 years ago
1
Add SeqPrep and Scythe to the benchmarks
#2
jdidion
closed
6 years ago
4
progress with "msg" option fails
#1
cokelaer
closed
8 years ago
1
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