User Tools

Site Tools


whatshap-software

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

whatshap-software [2018/06/27 13:39] (current)
aorth created
Line 1: Line 1:
 +====== WhatsHap ======
  
 +WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads.
 +
 +===== Information =====
 +
 +  * Version: 0.16
 +  * Added: June, 2018
 +  * Link: https://​whatshap.readthedocs.io/​en/​latest/​index.html
 +
 +===== Usage =====
 +
 +See which versions of whatshap are available:
 +<​code>​$ module avail whatshap</​code>​
 +
 +Load one version into your environment and run it:
 +<​code>​$ module load whatshap/​0.16
 +$ whatshap</​code>​
 +
 +===== Installation ======
 +
 +Notes from the sysadmin during installation:​
 +
 +<​code>​$ cd /tmp
 +$ module load python/​3.6.2
 +$ sudo mkdir -p /​export/​apps/​whatshap/​0.16
 +$ sudo chown aorth:aorth /​export/​apps/​whatshap/​0.16
 +$ python -m venv /​export/​apps/​whatshap/​0.16
 +$ . /​export/​apps/​whatshap/​0.16/​bin/​activate
 +$ pip3 install whatshap
 +$ sudo chown -R root:root /​export/​apps/​whatshap</​code>​
whatshap-software.txt · Last modified: 2018/06/27 13:39 by aorth