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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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Ways to shorten assembly time when using plasmid reference
#372
he-hai
opened
2 months ago
0
How to compare results from many strains?
#371
cgliss
opened
2 months ago
4
Error using nanopore reads as input
#370
Cat-Jane
opened
2 months ago
5
ERROR: Seq ID not found in reference sequence files provided for entry
#369
BrinleyL
closed
2 months ago
6
gdtools ANNOTATE TABLE format puts extra comma in header row
#368
dannagifford
closed
1 month ago
0
samtools included with patch
#367
alexmyczko
opened
4 months ago
1
Mutation not matching annotation
#366
erikwolfsohn
closed
5 months ago
3
bowtie2 subprocess using more CPU cores than allowed by -j option
#365
leowill01
closed
5 months ago
4
Including Junctions and Missing Coverage information when building a phylogenetic tree
#364
RayaRomm
opened
5 months ago
4
question about criteria for assigning genes_promoter to intergenic region
#363
gabypetrungaro
closed
5 months ago
4
How to Calculate the Frequency of IS Insertion Events
#362
miniluphy
closed
5 months ago
2
Polymorphism score to detect cross-sample contamination?
#361
KR0manova
closed
5 months ago
1
Generating new consensus sequence with variants
#360
james-weger
closed
8 months ago
2
Is -c the same as -r for single sequence references?
#359
padpadpadpad
closed
9 months ago
3
Problem in understanding breseq output (26-bp)2→1
#358
Subhajeet1997
closed
9 months ago
1
Identify linked mutations from mapped reads
#357
spleonard1
opened
9 months ago
2
Update bioconda link
#356
yoavram
closed
10 months ago
0
gdtools INTERSECT based on gene_name
#355
osekulovic
closed
9 months ago
4
A question about "gdtools COMPARE" html output
#354
adirot
closed
12 months ago
2
Cannot read reference alignment
#353
filifed
closed
12 months ago
1
annotation was blank
#352
kissboyxiao
closed
1 year ago
1
Hard drive fills entirely after running breseq for some time, until reboot
#351
Antovigo
closed
1 year ago
2
Error: Directory nonexistent. Code 512
#350
RpfR2000
closed
1 year ago
4
Complete genome needed?
#349
termithorbor
closed
1 year ago
5
Terminal width of 80
#348
swplotner
closed
9 months ago
3
Can't find expected R scripts
#347
jsa-aerial
closed
1 year ago
3
Errors preventing completion
#346
bensprung
closed
1 year ago
9
NA and delta frequncy of mutions using gdtools COUNT (breseq v0.37.1)
#345
xiaolinchu92
closed
1 year ago
3
0.37.1 binary throws "unable to execute bin/breseq: Bad CPU type in executable" on Intel Mac
#344
mdt1024
closed
1 year ago
1
Use GD tools apply to generate several distinct updated references with similar frequency variants from polymorphism mode
#343
spleonard1
closed
1 year ago
2
what is causing this error? "libc++abi: terminating with uncaught exception of type std::domain_error"
#342
zahraa992
closed
1 year ago
1
Add 'name' metadata to already complete run?
#341
dannagifford
closed
1 year ago
3
run stalling, but no specific error message
#340
Jessica1080
closed
1 year ago
2
no output.html file
#339
SoGUILL
closed
1 year ago
5
Error with `GLIBCXX_3.4.30' running breseq in conda environment on HPCC
#338
cyrusmallon
closed
1 year ago
2
NA frequency for a JC-based variant. What does it mean?
#337
vr1087
closed
1 year ago
2
What is the difference between intergenic and noncoding SNPs?
#336
galtoledano
closed
1 year ago
2
terminate called after throwing an instance of 'std::length_error'
#335
ck-theory
closed
1 year ago
3
No new junction prediction when using --aligned-sam
#334
vrohnie
closed
1 year ago
4
Output wihout .html files
#333
miniluphy
closed
1 year ago
3
gdtools problem
#332
ihara920
closed
1 year ago
2
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
9 months 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
1 year ago
4
Conda downloads older version
#326
antanij
closed
1 year ago
3
Use of term "dispersion" in coverage summary reporting is confusing
#325
rohanmaddamsetti
closed
1 year ago
1
FATAL ERROR
#324
airbender97
closed
1 year ago
1
Error(s) in GenomeDiff format. FILE when trying to add duplicate
#323
xiaolinchu92
closed
1 year ago
3
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