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katholt
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srst2
Short Read Sequence Typing for Bacterial Pathogens
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Instruction for the srst2_plots.R
#46
minisciencegirl
closed
8 years ago
1
A revision of the ARG-Annot database (ARGannot.r1.fasta)
#45
wanyuac
closed
8 years ago
0
A revision of the ARG-Annot database
#44
wanyuac
closed
9 years ago
2
Redundancy (CARB-2 and CARB-8 genes) in ARGannot.fasta
#43
wanyuac
closed
8 years ago
1
Update README.md
#42
swlong
closed
8 years ago
0
Update srst2.py
#41
niyunyun
closed
8 years ago
1
Crash when trying to create novel allele consensus fasta from ARG database
#40
swlong
closed
8 years ago
5
Discrepancy between top scoring allele in result file and consensus sequence file
#39
alex-m-a
closed
8 years ago
3
Crash during processing of large number of compiledResults.txt files into a single output
#38
swlong
closed
3 years ago
3
Sample column blank in output__mlst__XYZ__results.txt
#37
complexgenome
closed
9 years ago
2
Allow forward and reverse flags as file name
#36
complexgenome
closed
9 years ago
2
Analyzing NextSEq data
#35
tomitaMDU
closed
9 years ago
2
SRST2v0.1.5 crashes when using gene_db with only gene names in the FastA headers
#34
cglambert
closed
8 years ago
1
Rcode
#33
paolaflorez
closed
9 years ago
4
Fix for issue 25
#32
ppcherng
closed
9 years ago
1
mlst results file only contains header when running certain samples
#31
ppcherng
closed
9 years ago
1
replacing slashes with underscores in pileup filename
#30
ppcherng
closed
8 years ago
0
srst2.py throws error if allele has slash character
#29
ppcherng
closed
9 years ago
1
Patch to address issue #27
#28
Takadonet
closed
8 years ago
1
Miscalling alleles with only indels differences between variants
#27
Takadonet
closed
9 years ago
1
create_allele_pileup crashes if --output contained a directory path
#26
ppcherng
closed
9 years ago
1
VFDB_cdhit_to_csv.py throws KeyError for Mycobacterium
#25
ppcherng
closed
9 years ago
3
Problem with reading pileup using non-recommended versions of samtools & bowtie
#24
katholt
closed
9 years ago
8
Adding utility bash scripts for automating VFDB gene database generation
#23
ppcherng
closed
9 years ago
0
Fails on bowtie 2.2.x series, needs 2.1.0 only?
#22
tseemann
closed
9 years ago
2
fullgenes table not reporting all samples when multiple readsets run in serial
#21
katholt
closed
9 years ago
2
example.txt is missing the confident ST after line 106
#20
ppcherng
closed
9 years ago
1
getmlst.py crashes with a cryptic error message when downloading "Campylobacter fetus"
#19
ppcherng
closed
9 years ago
3
accommodate slashes in species names
#18
katholt
closed
9 years ago
1
download error
#17
livyuan
closed
9 years ago
3
allow multiple read sets per sample, merged to give single result
#16
katholt
closed
9 years ago
4
add example command and web link to the text printed upon installation
#15
katholt
closed
3 years ago
0
PIP doesn't have scipy listed as dependency
#14
tseemann
closed
9 years ago
4
Extract new allele sequence
#13
ConstantinV
closed
10 years ago
5
Change default behaviour to throw away pileups & final sorted bam
#12
katholt
closed
3 years ago
0
Allow bowtie2 versions higher than 2.1.0
#11
katholt
closed
9 years ago
1
Added option to report the consensus allele for genes where no exact mat...
#10
hdashnow
closed
10 years ago
2
Fixed error in argparse help message for min_coverage and max_divergence...
#9
bjpop
closed
10 years ago
1
Need a maximum divergence option to simplify gene reporting.
#8
katholt
closed
10 years ago
1
Gene detection reporting - top gene per gene symbol, rather than the top gene per cluster as intended
#7
katholt
closed
10 years ago
1
Update srst2.py
#6
swlong
closed
10 years ago
0
Typo in srst2.py causing VFDB searches to fail
#5
swlong
closed
10 years ago
1
Add example output to doc (as figure since tables don't display properly)
#4
katholt
closed
10 years ago
1
Add 'How it works' section to doc
#3
katholt
closed
10 years ago
1
error in forward/reverse read identification
#2
katholt
closed
10 years ago
1
default path to srst2 in the slurm_srst2.py script is 'srst2.py' but should be 'srst2'
#1
katholt
closed
10 years ago
1
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