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seroba-software [2018/11/17 23:57] (current)
aorth created
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 +====== seroba ======
 +SeroBA is a k-mer based Pipeline to identify the Serotype from Illumina NGS reads for given references. You can use SeroBA to download references from [[https://​github.com/​phe-bioinformatics/​PneumoCaT|PneumoCaT]] to do identify the capsular type of Streptococcus pneumoniae.
  
 +===== Information =====
 +
 +  * Version: 1.0.0
 +  * Added: November, 2018
 +  * Link: https://​github.com/​sanger-pathogens/​seroba
 +
 +===== Usage =====
 +
 +See versions which are available:
 +<​code>​$ module avail seroba</​code>​
 +
 +Load one version into your environment and run it:
 +<​code>​$ module load seroba/​1.0.0
 +$ seroba</​code>​
 +
 +===== Installation ======
 +Notes from the sysadmin during installation:​
 +
 +<​code>​$ cd /tmp
 +$ sudo mkdir -p /​export/​apps/​seroba/​1.0.0
 +$ sudo chown aorth /​export/​apps/​seroba/​1.0.0
 +$ python3.6m -m venv /​export/​apps/​seroba/​1.0.0
 +$ source /​export/​apps/​seroba/​1.0.0/​bin/​activate
 +$ module load MUMer/3.23
 +$ pip3 install ariba pymummer biopython pyyaml
 +$ pip3 install seroba
 +$ sudo chown -R root:root /​export/​apps/​seroba</​code>​
seroba-software.txt · Last modified: 2018/11/17 23:57 by aorth