Small fixes to metadata dictionary structure and population schemes. quastR now works.
continual improvements - contig files are trimmed to 200bp, and nodes are renamed with the fileName
continual improvements - rMLST can identify alleles. Needs to associate allele profiles with the master list of profiles.
rMLST can determine subtypes. There is an issue with the rMLST scheme, where certain alleles are reported as 'N' in the scheme, where they really look like they should be present.
insert sizes are estimated by lse.py
rMLST finds best reference genome. Pipeline is functional.
GAGE mode doesn't work. Everything else does now.
Merge pull request #1 from adamkoziol/master

Updating OLC-Bioinformatics