pop_genome

DESCRIPTION

A collection of scripts used for comparative population genomics analyses of large microbial genome datasets. Many of the scripts are build uponITEP, which is a toolset for pangenome analysis.

DEPENDENCIES

Depending on the script:

• BioPerl
• ITEP
• SNAP
• PAML
• Arlecore
• Mowgli
• Ranger-DTL
• Mothur
• PhiPack
• sqlite

INSTALLATION

git clone https://github.com/nyoungb2/pop_genome.git

To install this module, run the following commands:

perl Build.PL
./Build
./Build test
./Build install

Or just add the bin folder to your $PATH. This link provides more info on adding to your $PATH.

Getting help

Script documentation

SCRIPT.pl -h
perldoc SCRIPT.pl

Post issues on GitHub

[Issues](https://github.com/nyoungb2/pop_genome/issues)

ITEP Extensions

Scripts named as "ITEP_*" require ITEP (or files produced by ITEP) to run.

Some features

• Convert the ITEP geneInfo table to a gff3 file:
• ITEP_geneInfo2gff.pl
• Get info on how far apart genes are on each genome
• ITEP_geneInfo2scaffoldDist.pl
• For draft genes: get the distance of a gene to a contig end (helps for finding artificial gene trucations)
• ITEP_geneInfoDist2ContigEnd.pl
• Make a ITOL compatible metadata table of gene copies per taxon-gene_cluster
• ITEP_geneInfo2ITOL.pl
• My own alignment and phylogeny inference pipeline to use with ITEP
• ITEP_align-tree.pl
• Add COG info to a table containing PED IDs (eg., the geneInfo table)
• ITEP_clusterAddCOG.pl

Other Scripts

These scripts provide convenient methods for using many population genomics software on large datasets.

Many of these were used for the analysis in: 'N.D. Youngblut, J.S. Wirth, J.R. Henriksen , W.W. Metcalf, R.J. Whitaker Genomic and phenotypic differentiation among Methanosarcina mazei populations from Columbia River sediment, in prep'

Calculating Fst, mean sequence identity, & dN/dS for each ITEP sequence cluster

• arlecore_Fst_batch.pl
• seqID_byPop.pl
• SNAP_batch.pl

Batch runs of Mowgli

• Mowgli_batch.pl

Parsing output from the Quartet Decomposition Server

• quartetDecomp_byPop.pl
• quartetDecomp_distCut.pl

Make a database of output from multiple Ranger-DTL runs

• ranger-dtl_parse.pl
• ranger-dtl_parse_ITOL.pl
• rdtl-db_*

Calculate feature density for a Circos feature file

• circos_featDensity.pl

LICENSE AND COPYRIGHT

Copyright (C) 2013 Nick Youngblut

This program is free software; you can redistribute it and/or modify it under the terms of either: the GNU General Public License as published by the Free Software Foundation; or the Artistic License.

See Lhttp://dev.perl.org/licenses/ for more information.