issues
search
immcantation
/
presto
pRESTO is part of the Immcantation analysis framework for Adaptive Immune Receptor Repertoire sequencing (AIRR-seq). pRESTO is a bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.
https://presto.readthedocs.io
GNU Affero General Public License v3.0
0
stars
0
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Add barcode length parameter for MaskPrimers
#94
ggabernet
opened
3 weeks ago
0
Jobs submitted on the cluster cannot be run in multiple threads
#93
ssnn-airr
closed
3 months ago
2
Output of AssemblePairs.py sequential and align is the same
#92
ssnn-airr
closed
7 months ago
3
Bio.pairwise2 deprecation
#91
ssnn-airr
closed
9 months ago
2
create pyproject.toml
#90
ssnn-airr
closed
11 months ago
1
Huge processing times for CollapseSeq
#89
ssnn-airr
opened
1 year ago
0
Add U to T character mapping in scoring functions
#88
ssnn-airr
closed
2 years ago
1
Add unique identify to start of read names for downstream analysis
#87
ssnn-airr
closed
2 years ago
2
AssemblePairs.py sequential fails when input file lists are added under the '-1' and '-2' arguments.
#86
ssnn-airr
closed
3 years ago
4
UMI is known but primers are not
#85
ssnn-airr
closed
2 years ago
2
Manage special characters in the header annotations
#84
ssnn-airr
closed
2 years ago
6
Fatal `EstimateError.py set` error after progress bar reads 100%
#83
ssnn-airr
closed
2 years ago
12
Option to increase cd-hit-est memory limit
#82
ssnn-airr
closed
2 years ago
3
Jiang 2013 example script incompatible with Mac OS
#81
ssnn-airr
opened
3 years ago
3
Is the pip3 install broken on macOS?
#80
ssnn-airr
closed
3 years ago
5
AssemblePairs.py align -1 ERR346600_2.fastq -2 ERR346600_1.fastq
#79
ssnn-airr
closed
3 years ago
3
Usage on bulk RNA-seq samples
#78
ssnn-airr
closed
3 years ago
2
Bio.Alphabet import error for Biopython 1.78
#77
ssnn-airr
closed
3 years ago
2
Incompatibility with biopython v1.78
#76
ssnn-airr
closed
4 years ago
2
Applications.py using a deprecated method from Bio
#75
ssnn-airr
closed
4 years ago
5
Redesign CollapseSeq algorithm
#74
ssnn-airr
opened
4 years ago
5
Read configuration discovery and debug example docs
#73
ssnn-airr
opened
4 years ago
0
error in Multiprocessing.py with singularity
#72
ssnn-airr
closed
2 years ago
4
AssemblePairs get stuck
#71
ssnn-airr
closed
4 years ago
6
Read quality = 0 stops FilterSeq
#70
ssnn-airr
closed
4 years ago
2
Add example workflow for UMI following primer
#69
ssnn-airr
opened
5 years ago
0
Maybe add vsearch merge wrapper to AssemblePairs
#68
ssnn-airr
opened
5 years ago
0
Should --scanrev be default for AssemblePairs?
#67
ssnn-airr
opened
5 years ago
0
Add simple preprocessing workflow
#66
ssnn-airr
opened
5 years ago
1
AssemblePairs hanging (most likely due to blastn?)
#65
ssnn-airr
opened
6 years ago
10
Removing pandas from countMismatches in EstimateError.py
#64
ssnn-airr
closed
6 years ago
2
Running out of memory with CollapseSeq
#63
ssnn-airr
closed
6 years ago
6
Tools should not write empty fail files
#62
ssnn-airr
closed
6 years ago
1
Update example workflows for presto v0.5.7
#61
ssnn-airr
closed
6 years ago
2
Error during BuildConsensus
#60
ssnn-airr
closed
6 years ago
7
UnifyHeaders consensus Log
#59
ssnn-airr
closed
6 years ago
1
Add more details to UnifyHeaders log
#58
ssnn-airr
closed
6 years ago
1
Add check to AssemblePairs for reads shorter than --minlen
#57
ssnn-airr
closed
6 years ago
1
Add AbSeq workflow to docs
#56
ssnn-airr
closed
7 years ago
1
Add subcommands to MaskPrimers to deal with data for which primers are unavailable
#55
ssnn-airr
closed
6 years ago
9
fastq file has unrecognized type
#54
ssnn-airr
closed
7 years ago
9
EstimateError.py pandas bug.
#53
ssnn-airr
closed
7 years ago
1
runUClust supports vsearch 2.4.2 but not usearch v9.2
#52
ssnn-airr
closed
7 years ago
2
usearch -makeudb_usearch no longer supported
#51
ssnn-airr
closed
7 years ago
2
vsearch runUblast incompatibility
#50
ssnn-airr
closed
7 years ago
2
Add align-to-reference rollover mode to AssemblePairs
#49
ssnn-airr
closed
7 years ago
2
AssemblePairs: error: unrecognized arguments: --aligner blastn
#48
ssnn-airr
closed
7 years ago
2
presto.Application API docs are not rendering correctly
#47
ssnn-airr
closed
7 years ago
1
Allow AssemblePairs-reference to use gapped references
#46
ssnn-airr
closed
7 years ago
2
Replace usearch with an open source tool in AssemblePairs-reference
#45
ssnn-airr
closed
7 years ago
4
Next