README

/PURPOSE/
Various scripts to manipulate genomes and metagenomes on the SHARCNET HPC cluster
Including BLAST, BOWTIE, clustering (single linkage, MCL), aligning, treeing, etc.

These scripts are sometimes trivial, generally poorly written and often poorly documented
mea culpa

/AUTHORS/
Written by Eric Collins based on an original set of scripts by Hugh Merz


/EXAMPLES/

A typical workflow might go something like....

1) Identify genomes of interest, e.g. 'Alteromonadales'
2) make blastlists and taxalists:
   ./gettaxa.pl Alteromonadales AL
3) do all-vs-all blasts for Alteromonadales
   ./blaster4.pl blastlist-Alteromonadales
4) cluster genomes using single-linkage algorithm at several cutoffs of evalue/length fraction
   ./cluster.sh AL_110001 taxalist-Alteromonadales-with-plasmids
5) make gene matrix from cluster list
   ./genematrix.pl taxalist-Alteromonadales-with-plasmids AL_110001.1e-10_0.7_long_on.cluster_list AL_110001
6) identify single-copy core genes
   R CMD BASH singlecopy.R
7) make concatenated alignments and ML tree from single-copy core genes
   ./clustercattree.sh AL_110001.1e-10_0.7_long_on.single-copy.csv taxalist-Alteromonadales-with-plasmids AL_110001.1e-10_0.7_long_on.cluster_list AL_110001

TODO:
lots