issues
search
katholt
/
srst2
Short Read Sequence Typing for Bacterial Pathogens
Other
123
stars
65
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Question regarding samtools pileup parameters
#96
andreott
closed
3 years ago
0
Reference file does not seem to be a FASTA file
#95
bc2zb
closed
6 years ago
2
Using new ARG-ANNOT v3 database
#94
hjb60
closed
6 years ago
5
Removed two tetR alleles from the r2 database
#93
wanyuac
closed
6 years ago
0
grep gene db syntax error
#92
IshwaryaMullaiSelvapandian
opened
6 years ago
1
--threads param not getting passed to samtools?
#91
russellsmithies
closed
6 years ago
1
Adaptation of SRST2:
#90
EisenRa
closed
6 years ago
1
cdhit_to_csv.py and IndexError: list index out of range
#89
TreeT2
closed
3 years ago
1
VFDB_cdhit_to_csv.py error
#88
Wang-Jing-NZ
closed
7 years ago
2
IndexError: list index out of range
#87
bikongxingchen0811
closed
5 years ago
3
Add output folder option for getMLST.py
#86
alegione
opened
7 years ago
0
Discrepancy between the wget commands and the srst2 command line.
#85
Redmar-van-den-Berg
closed
6 years ago
1
Delimiter warning for Acinetobacter MLST
#84
davidwcleary
closed
5 years ago
3
More duplicates in EcOH.fasta
#83
tseemann
closed
3 years ago
0
creating srst2 executable
#82
najoshi
opened
7 years ago
2
failed to plot figure using R
#81
xthua
closed
3 years ago
3
read depth calculation
#80
abrozzi
opened
7 years ago
2
Provide FASTA via --gene_db but SRST2 seems to expect bowtie index?
#79
mw55309
closed
7 years ago
2
Error
#78
lskatz
closed
7 years ago
1
assembled contigs as input files for srst2?
#77
MostafaYA
closed
7 years ago
1
distutils does not support entry_points
#76
ericenns
closed
3 years ago
0
Error with gene database made from VFDB: vertical bars in headers
#75
amilesj
closed
7 years ago
1
ValueError("Inputs must not be empty") when running srst2 invoking --input_pe
#74
lilipeng
opened
7 years ago
1
Different MLST result when re-running SRST2 after adding in new alleles
#73
swlong
opened
7 years ago
3
Introducing the ARG-ANNOT r2 database and editions to the documentation
#72
wanyuac
closed
6 years ago
0
Could not determine forward/reverse read status for input file
#71
FelipeMelis
closed
7 years ago
1
MANIFEST.in does not include the data folder
#70
andersgs
closed
3 years ago
0
RuntimeWarning: floating point number trucated to an integer
#69
alantsangmb
closed
3 years ago
9
Change the database to CARD
#68
KatherineJ-H
closed
6 years ago
2
VFDB clusterid naming convention problem, KeyError: '51__map__map_ATCC'
#67
toddknutson
closed
7 years ago
2
file scores_vs_expected.py seems missing
#66
PWSmit
closed
8 years ago
3
Why are my isolate names appended with a '?' in some cases but not all?
#65
schultzm
closed
8 years ago
2
EcOH.fasta has 47 duplicate sequences & some inconsistences
#64
tseemann
closed
8 years ago
1
Update SLURM generator for use on Helix cluster
#63
rrwick
closed
8 years ago
0
A set of improvements fixing problems with MLST on Klebsiella pneumoniae genomes
#62
andreyto
closed
8 years ago
1
The module logging is necessary for slurm_srst2.py
#61
wanyuac
closed
7 years ago
1
Addition of the module logging is necessary for the script
#60
wanyuac
closed
7 years ago
1
Error in step: Using the VFDB Virulence Factor Database with SRST2
#59
schultzm
closed
8 years ago
2
Nb. User error using getmlst.py script
#58
swlong
closed
8 years ago
1
Error with bowtie
#57
edgarom
closed
7 years ago
2
single end and paired end reads for a sample
#56
cytang19
closed
8 years ago
2
grep gene name syntax error
#55
cytang19
closed
8 years ago
1
global name 'seq_id' is not defined error
#54
AlefNeem
closed
8 years ago
2
SRST2 installation problem with multiple Bowtie versions
#53
patms
opened
8 years ago
1
UnboundLocalError for VFDB_cdhit_to_csv.py
#52
sarahpenir
closed
8 years ago
4
Get samtools and bowtie executables from env variables (with tests)
#51
bewt85
closed
8 years ago
0
Get samtools and bowtie executables from env variables
#50
bewt85
closed
8 years ago
1
Use a specific version of samtools (and others)
#49
bewt85
closed
8 years ago
6
Couple of fixes for
#48
SionBayliss
closed
8 years ago
1
Difference in log files for negatives when using gene_db
#47
kajcox
opened
8 years ago
2
Previous
Next