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broadinstitute
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StrainGE
strain-level analysis tools
BSD 3-Clause "New" or "Revised" License
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Bump actions/download-artifact from 3 to 4.1.7 in /.github/workflows
#41
dependabot[bot]
opened
1 week ago
0
Running StrainGR call with refs_concat.fasta results TypeError: 'NoneType' object is not subscriptable
#40
sjmiller-sahmri
opened
2 weeks ago
1
'VariantCallData' object has no attribute 'bad_read'
#39
sconlan
opened
6 months ago
0
Error in customising database through straingst
#37
sahilrishav2
closed
6 months ago
4
StrainGR identifies SNVs in samples where StrainGST did not detect a strain
#36
kebow
opened
8 months ago
0
straingr prepare-ref gives warning about missing metadata each time it is run
#35
joelewis101
closed
9 months ago
1
Installation error with incompatible scipy version
#34
parul-sharma
opened
11 months ago
1
Error due to five indices for possible alleles, rather than six
#33
gavinmdouglas
closed
11 months ago
2
ValueError: cannot set null allele
#32
wwood
opened
1 year ago
0
cannot convert float NaN to integer
#31
nick-youngblut
opened
1 year ago
2
ZeroDivisionError: division by zero when setting up DB for acinetobacter genus
#30
AdrianLimaG
closed
1 year ago
1
Preparing a DB for StrainGR
#29
wwood
opened
1 year ago
0
How do you define the unique reads
#28
StickHu
opened
1 year ago
0
Can we run on non complete genomes
#26
SilasK
closed
1 year ago
1
Installation instructions do not work with micromamba
#25
tstraub89
opened
1 year ago
1
'utf-8' codec can't decode byte 0x89 in position 0
#24
nick-youngblut
closed
1 year ago
1
ncbi-genome-download-The download content is empty!
#23
qkqk-hub
closed
1 year ago
2
straingr compare all vs all deon't create output file.
#21
SilasK
opened
1 year ago
1
mummer is not part of the conda env.
#20
SilasK
closed
1 year ago
1
prepare-ref looks for metadata file inside fasta file repository, with no option to parametrise this
#19
SilasK
opened
1 year ago
1
typo
#18
SilasK
closed
1 year ago
1
Division by Zero Error during Database Creation Step (straingst kmersim)
#17
autpereira
closed
1 year ago
2
Change path template
#16
Ahmedbargheet
opened
2 years ago
0
Prepare a concatenated reference
#15
Ahmedbargheet
closed
2 years ago
1
Fix kmerize --filter crash
#14
w1bw
closed
2 years ago
0
"straginst kmerize --filter ..." crashing
#13
w1bw
closed
2 years ago
2
KeyError when running straingst cluster
#12
samnooij
closed
10 months ago
16
Stopiteration
#11
Ahmedbargheet
closed
2 years ago
3
issues with straingr view: --vcf and --verbose-vcf arguments produced no or unexpected output
#10
biolene
closed
2 years ago
3
Use of BWA-MEM2 or BWA-MEME
#9
nick-youngblut
closed
2 years ago
1
straingr prepare-ref => .fa.gz.fa.gz does not exist!
#8
nick-youngblut
closed
2 years ago
3
straingst run => non-standard tsv
#7
nick-youngblut
closed
2 years ago
2
straingst kmerize => parallel
#6
nick-youngblut
closed
2 years ago
1
added parallel processing for prepare_strainge_db.py
#5
nick-youngblut
opened
2 years ago
0
prepare_strainge_db.py
#4
nick-youngblut
opened
2 years ago
3
Can I use my own genomes/data and skip the ncbi-download phase?
#3
drelo
closed
3 years ago
5
ncbi-genome-download `ERROR: No entry for file ending in '_rm.out.gz'`
#2
drelo
closed
3 years ago
2
Python packaging improvements
#1
lrvdijk
closed
5 years ago
0