https://github.com/sjackman/snoove

Create a dendrogram from genome sequencing data
https://github.com/sjackman/snoove

Last synced: about 1 month ago
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Create a dendrogram from genome sequencing data

• Host: GitHub
• URL: https://github.com/sjackman/snoove
• Owner: sjackman
• Created: 2013-02-28T23:23:07.000Z (almost 12 years ago)
• Default Branch: master
• Last Pushed: 2013-07-08T17:48:43.000Z (over 11 years ago)
• Last Synced: 2024-10-13T20:46:41.672Z (2 months ago)
• Language: Perl
• Size: 180 KB
• Stars: 1
• Watchers: 3
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
Pathogen Variant Calling Pipeline

=================================

This pipeline aligns reads to a reference and calls variants using BWA and samtools.

Written by Shaun Jackman 

Required Software

=================

 * BWA

 * samtools

 * tabix

 * FastTree

Input

=====

* FASTQ files of short read sequencing data

* A reference genome sequence

Output

======

 * a BAM file of reads aligned to the reference

 * a VCF file of variant calls

 * a FASTA file of the genotype of those variants

 * a dendrogram derived from those genotypes