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nanopolish-software

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

Usage

See versions which are available:

$ module avail nanopolish

Load one version into your environment and run it:

$ module load nanopolish/0.10.2
$ nanopolish help

Installation

Notes from the sysadmin during installation:

$ 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
nanopolish-software.txt · Last modified: 2018/11/18 01:20 by aorth