sistr_cmd
sistr_cmd copied to clipboard
phac-nml
SISTR (Salmonella In Silico Typing Resource) command-line tool
as the title above. We tested with ATCC 9150 type strain it gave us the expected results. But on some of our isolates the serogroup assignment is D1. We could...
error
./sistr Traceback (most recent call last): File "./sistr", line 7, in from sistr.sistr_cmd import main File "/home/tools/anaconda3/lib/python3.7/site-packages/sistr/sistr_cmd.py", line 14, in from sistr.src.blast_wrapper import BlastRunner File "/home/tools/anaconda3/lib/python3.7/site-packages/sistr/src/blast_wrapper/__init__.py", line 9, in from...
How to reproduce: ``` wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/007/463/835/GCA_007463835.1_PDT000542330.1/GCA_007463835.1_PDT000542330.1_ge nomic.fna.gz gunzip GCA_007463835.1_PDT000542330.1_genomic.fna.gz sistr -m --qc -f tab -t 2 -i GCA_007463835.1_PDT000542330.1_genomic.fna GCA_007463835.1_PDT000542330.1 -o GCA_007463835.1_PDT000542330.1 Traceback (most recent call last): File "/usr/local/bin/sistr", line 8,...
In SISTR v1.1.1. the O51 antigen prediction might be jeopardized as confirmed by recent PulseNet submission. The SISTR v1.1.1 in-silico prediction provided IIIb **51**:k:z35 while traditional serotyping predicted IIIb **47**:k:z35...
Dear Developers, We recently used sistr to serotype some salmonella samples. We realized that the Sistr serovar overall prediction is different from the RefSeq match. In such instances, which serovar...
In the next SISTR release check serogroup predictions. In version 1.1.1 the predicted O9,46 antigen was reported as D1 serogroup instead of expected D2 for PulseNet sampleID 21-01676. Not critical,...
Hello SISTR users and *in silico* serotypers! Do you have any *Salmonella* genomes with trustworthy serovar info? Would you like SISTR to provide better serovar predictions? You can help by...
SISTR codebase should have tests made for automatic testing of new functionality
> Output a `WARNING` if < 10 representatives in database for a serovar
Hello, We've isolated some subsp salamaes for one of our projects. I have a few questions about the SISTR output for these isolates: sample | cgmlst_found_loci | cgmlst_matching_alleles | cgmlst_subspecies...
