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barricklab
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breseq
breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data. It is intended for haploid microbial genomes (<20 Mb). breseq is a command line tool implemented in C++ and R.
http://barricklab.org/breseq
GNU General Public License v2.0
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gdtools (v0.37.1) still have a problem of the difference between Locus and feature in the genebank file.
#331
ihara920
closed
1 year ago
1
Feature request: access empirical error distribution command as standalone
#330
osilander
closed
1 year ago
3
Expected resolution of mutation frequency calling in population mode given a certain read depth
#329
mretier
closed
1 year ago
2
Unassigned new junction evidence with NA reads
#328
mretier
closed
1 year ago
2
FASTQ sequence record does not begin with @NAME line
#327
Barrington-wustl
closed
2 years ago
4
Conda downloads older version
#326
antanij
closed
2 years ago
3
Use of term "dispersion" in coverage summary reporting is confusing
#325
rohanmaddamsetti
closed
2 years ago
1
FATAL ERROR
#324
airbender97
closed
2 years ago
1
Error(s) in GenomeDiff format. FILE when trying to add duplicate
#323
xiaolinchu92
closed
2 years ago
3
fatal error while tabulating read counts - read quality above maximum value?
#322
peterculviner
closed
2 years ago
10
annotation error
#321
he-hai
closed
2 years ago
1
rejected polymorphism call predicted as 100% frequency consensus call
#320
rohanmaddamsetti
closed
2 years ago
4
Unable to predict genomic insertion if it overlaps a deletion
#319
vr1087
closed
1 week ago
1
Variant prediction in regions with overlapping unique and repeat coverage
#318
vr1087
closed
2 years ago
2
breseq for nanopore reads
#317
kesava31
closed
1 year ago
2
Update version at bioconda to 0.37
#316
wwarriner
closed
2 years ago
1
Non-intuitive WARNING + FATAL ERROR when using multiple references with same-name LOCUS definitions
#315
dannagifford
closed
2 years ago
7
Mixed populations of the same 'species' - two complete reference genomes
#314
dannagifford
closed
2 years ago
4
breseq randomly hangs
#313
vr1087
closed
2 years ago
1
Broken Links
#312
miracleburt
closed
2 years ago
5
Meaning of arrows at the output file
#311
galtoledano
closed
2 years ago
1
Meaning of ‡ symbol in breseq annotation output
#310
Burmeistera
closed
2 years ago
2
Segmentation fault in samtools sort
#309
ellieharrisn
closed
1 year ago
8
How to make a TSV format for compare.
#308
khoriba
closed
2 years ago
1
terminate called after throwing an instance of 'std::invalid_argument'
#307
898289687
closed
2 years ago
10
Struggling to download
#306
Barrington-wustl
closed
2 years ago
1
Error while installing breseq using conda
#305
joshuamiranda007
closed
2 years ago
2
Fatal error during my analysis
#304
sangdoy2
closed
2 years ago
2
How to merge multiple mutations in the same position in a time series?
#303
loukesio
closed
1 week ago
1
Directly process .tab to final .html output?
#302
wichne
closed
2 years ago
1
Using -s option for reference file
#301
hm22rice
closed
2 years ago
5
Breseq suitable for Basidiomycetes
#300
termithorbor
closed
2 years ago
1
ERROR Could not determine version of installed executable "R".
#299
ppat818
closed
2 years ago
6
Error: Repeat feature must have only one location
#298
tamarahalter
closed
2 years ago
2
How to merge multi-sample result into one file to get a summarized summary file for all samples for Insertion sequences?
#297
safinaARK
opened
2 years ago
0
feature request: long-read sequencing input
#296
wmoebius
closed
1 year ago
3
Fatal error running bowtie2 using default conda install breseq
#295
spleonard1
closed
2 years ago
4
Help me understand Unassigned new junction evidences
#294
BatistaB
closed
2 years ago
4
Question on Inversion predictions
#293
vr1087
closed
1 week ago
4
std::bad_alloc
#292
khoriba
closed
2 years ago
5
FATAL ERROR: Attempt to translate codon without three bases
#291
MarekSvob
closed
2 years ago
9
I can't Run Breseq (I got a problem with R)
#290
BatistaB
closed
3 years ago
3
gdtools PHYLOGENY: dnapars not found, even though phylip is installed
#289
dannagifford
closed
2 years ago
2
Fatal error during analysis
#288
khoriba
closed
2 years ago
8
Feature Request - add AD,DP to GD COMPARE output
#287
kullrich
closed
1 week ago
6
gdtools REMOVE error
#286
scientiff
closed
3 years ago
2
Compare Breseq analysis from closed reference genome and draft control genome
#285
AshleySchumann
closed
3 years ago
3
windows (wsl) installation issue
#284
kushankur
closed
3 years ago
1
compare tables should always display sample names used to generate them
#283
danieldeatherage
opened
3 years ago
1
How to get read counts for all variants relative to reference?
#282
iaincambeul
closed
3 years ago
5
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