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Parsnp
Dreycey Albin edited this page May 16, 2019
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- Author: Dreycey Albin
- Date: 05/09/2019
- Updates: NAME (DATE): update descr; NAME (DATE): update descr,
- Program for genome alignment
- documentation (website): https://harvest.readthedocs.io/en/latest/content/parsnp/
- documentation (publication): URL TO PUBLICATION
- installation for MacOS
wget https://github.com/marbl/parsnp/releases/download/v1.2/parsnp-OSX64-v1.2.tar.gz;
tar -xvf parsnp-OSX64-v1.2.tar.gz
- installation for Linux
wget https://github.com/marbl/parsnp/releases/download/v1.2/parsnp-Linux64-v1.2.tar.gz;
tar -xvf parsnp-Linux64-v1.2.tar.gz
genomes, contigs, or scaffolds for aligning.
A directory containing the following files:
parsnp.ggr
parsnp.tree
parsnp.xmfa
parsnpAligner.ini
parsnpAligner.log
files provided by parsnp
and
wget https://harvest.readthedocs.io/en/latest/_downloads/mers49.tar.gz
./parsnp -d mers49 -r ref/EMC_2012.gbk.fna -c -p 10 -o outdir_1 > outlog_1.txt -c
parsnp.ggr
parsnp.tree
parsnp.xmfa
parsnpAligner.ini
parsnpAligner.log
These are a growing collection of manuals for commonly used bioinformatics tools.
Just go to the page for the tool you are trying to use, and scroll through the page to download and install. That simple. The goal is to add extra documentation for using these tools, in addition to what is already supplied by the manual pages for the programs.