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Serovar predictions from whole-genome sequence assemblies by determination of antigen gene and cgMLST gene alleles using BLAST. Mash MinHash can also be used for serovar prediction.


Show all available versions of sistr:

$ module avail sistr

Load a particular version of sistr and run it:

$ module load sistr/1.0.2
$ sistr -h


Notes from the sysadmin during installation:

$ module load python/3.6.2
$ sudo mkdir -p /export/apps/sistr/1.0.2
$ sudo chown aorth /export/apps/sistr/1.0.2
$ python -m venv /export/apps/sistr/1.0.2
$ . /export/apps/sistr/1.0.2/bin/activate
$ pip install --upgrade pip
$ pip install wheel
$ pip install numpy pandas
$ pip install sistr_cmd
$ sudo chown -R root:root /export/apps/sistr/1.0.2
sistr-software.txt · Last modified: 2018/01/15 17:15 by aorth