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nanopolish-software [2018/11/18 01:20] (current)
aorth created
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 +====== nanopolish ======
 +Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications,​ call SNPs and indels with respect to a reference genome and more (see Nanopolish modules, below).
  
 +===== Information =====
 +
 +  * Version: 0.10.2
 +  * Added: November, 2018
 +  * Link: https://​github.com/​jts/​nanopolish
 +
 +===== Usage =====
 +
 +See versions which are available:
 +<​code>​$ module avail nanopolish</​code>​
 +
 +Load one version into your environment and run it:
 +<​code>​$ module load nanopolish/​0.10.2
 +$ nanopolish help</​code>​
 +
 +===== Installation ======
 +Notes from the sysadmin during installation:​
 +
 +<​code>​$ cd /tmp
 +$ git clone --recursive https://​github.com/​jts/​nanopolish.git
 +$ cd nanopolish
 +$ git checkout v0.10.2
 +$ make
 +$ sudo mkdir -p /​export/​apps/​nanopolish/​0.10.2
 +$ sudo chown -R aorth:aorth /​export/​apps/​nanopolish/​0.10.2
 +$ cp -r bin docs nanopolish nanopolish_test scripts README.md LICENSE /​export/​apps/​nanopolish/​0.10.2
 +$ python3.6m -m venv /​export/​apps/​nanopolish/​0.10.2
 +$ source /​export/​apps/​nanopolish/​0.10.2/​bin/​activate
 +$ pip3 install biopython pysam
 +$ sudo chown -R root:root /​export/​apps/​nanopolish/​0.10.2</​code>​
nanopolish-software.txt · Last modified: 2018/11/18 01:20 by aorth