katholt srst2 issues - Githubissues

katholt / srst2

Short Read Sequence Typing for Bacterial Pathogens

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Allele typing error

#146 sydelstan opened 2 months ago
0
Latest version of bowtie2

#145 lskatz opened 3 months ago
0
custom databases - manual intervention required to complete code for sequence reads

#144 pjbiggs opened 5 months ago
0
Github and Conda version inconsistencies

#143 jvhagey opened 5 months ago
0
Error in output when a gene contains a parentheses

#142 nvlachos opened 6 months ago
0
confusing or incorrect scoring leads to mis-called allele

#141 mikeyweigand opened 10 months ago
0
Indel variation in reference alleles lead to sporadic ST miscalls for S. aureus

#140 keyfm opened 1 year ago
0
SyntaxError when running srst2

#139 cpavloud opened 1 year ago
1
urllib2.URLError:

#138 jvhagey opened 2 years ago
0
output

#137 daoerxianqiao opened 2 years ago
0
Neisseria Gonorrhoeae

#136 Kanyerezi30 opened 2 years ago
0
srst2_and_bowtie2

#135 MariaPerezVazquez closed 3 years ago
1
fix typo in README.md

#134 pmenzel closed 3 years ago
1
Proposal for compatibility with Biopython 1.78

#133 emollier closed 3 years ago
3
"ecoli.txt"

#132 Jeni05 closed 3 years ago
1
Gene typing gene results contain last hit of the list and not the best hit

#131 mdiricks opened 3 years ago
0
password request

#130 Jeni05 closed 3 years ago
1
Clustering CARD database

#129 arooney13 closed 3 years ago
4
Minor fix on line 17

#128 kant opened 3 years ago
1
Different naming from Resfinder CGE db

#127 deearahman closed 4 years ago
3
databases not updated

#126 ptapiar closed 3 years ago
1
Using srst2 for metagenomic screening

#125 Anto007 closed 3 years ago
1
VFDB cannot be executed from the middle.

#124 Iwashita-N closed 3 years ago
0
Same output entries from db

#123 dcm9123 closed 3 years ago
1
Please port to Python3

#122 tillea opened 4 years ago
2
KeyError with one header in CARD

#121 blue-moon22 closed 5 years ago
1
results filter for antibiotic resistance genes

#120 aslangabriel closed 5 years ago
3
conda install failed

#119 keyfm closed 5 years ago
3
read mapping multiple references?

#118 dcm9123 closed 5 years ago
1
Primer removal?

#117 dcm9123 closed 3 years ago
0
Output reports truncation when none is present

#116 cizydorczyk closed 3 years ago
0
VFDB Parse the cluster output and tabulate the results using the specific Virulence gene DB compatible script:

#115 aslangabriel opened 5 years ago
3
VFDB database problem

#114 aslangabriel closed 5 years ago
3
list index out of range with srst2.py

#113 anuravi1234 opened 5 years ago
3
add mcr alleles to resistance DB

#112 katholt closed 3 years ago
1
result interpretation

#111 capricy closed 5 years ago
1
Any convenient script for AMR-based heat map?

#110 Anto007 closed 5 years ago
1
Add --label option instead of guessing from read filenames

#109 tseemann opened 5 years ago
0
Meera make python3 compatible

#108 Meera-Srinivasan opened 5 years ago
1
Assess multiple/all MLSTs in a single run, rather than a single species MLST?

#107 jake9115 closed 5 years ago
4
MLST for diploid microbes

#106 labrat9 closed 5 years ago
1
running srst2 on python3

#105 ssarria closed 6 years ago
2
Installation error

#104 jhaan1027 closed 6 years ago
0
read input problems

#103 JeremyHorst closed 6 years ago
1
Using paired end and single end reads

#102 abouska closed 6 years ago
1
getmlst.py error?

#101 tsekizuka closed 5 years ago
1
Remove sample name parsing which doesn't work when directories have .…

#100 ericenns opened 6 years ago
0
Cannot parse strain name when '.' in file path

#99 Takadonet opened 6 years ago
3
Handling of empty alignment

#98 andreas-wilm closed 3 years ago
1
ARGannot.r1 E. coli chromosomal genes

#97 cahlstrom closed 6 years ago
1