The sispa-related from jcvi-cloud

sispa-related's Introduction

SISPA Post-Processing Perl Scripts
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vcf_snv.pl 
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Description:

This script takes a VCF file from kSNP and does the following:

 1) Filter VCF file to remove recombinant regions
 2) Creat a SNV matrix (snv_matrix.txt), only retaining rows that have at least the threshold(ie. 90%) of genomes present
 3) Create a SNV Fasta file and Phylip file for each genome (vcf_snv.fasta, vcf_snv.phy)
 4) Run raxML 

create_rpkm_matrix.pl
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Description:

This script takes a list of Fasta file reads and runs blastn against a provided antibiotic resistance (abR) gene database. 
It then generates a matrix of RPKM values for each gene (row) and genome (column).     

Requirements
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These scripts require a config file to be passed in. This config files requires the user to list the location of where
four external 3rd party tools are installed on their machines. The required 3rd party tools are:

raxmlHPC: https://github.com/stamatak/standard-RAxML
vcftools: http://vcftools.sourceforge.net/
formatdb*
blastall*

Note: formatdb and blastall are no longer supported by NCBI as they've switched to BLAST+. create_rpkm_matrix.pl uses the legacy blastall. If you do not have these installed you can ran blast+ on your reads outside of this script and place them in the output directory. They must be in -m8 format. Label the blast files <genome name>.blast and the script will recognize them and will create a RPKM value matrix.

Use the config.txt that was included in this package OR copy the text below to a new text file and change the install
paths accordingly:

raxmlHPC:/usr/local/bin/raxmlHPC
vcftools:/usr/local/bin/vcftools
formatdb: /usr/local/bin/formatdb
blastall:/usr/local/bin/blastall

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