Version 1.1.0
-
uses new database format
species_ids now include the genus and species (ex: Bacteroides_vulgatus_57955)
pan-genome genes now defined at 95% identity threshold
removed 16S database for species profiling
for other info, see: http://lighthouse.ucsf.edu/MIDAS/README.txt -
run_midas.py and merge_midas.py require specification of database path
enables users to specify their own database, or different versions of default database -
improved run_midas.py snps
-increased speed and decreased memory usage
-fixed bug when computing depth at sites with N's
-fixed bug when reference allele is not ATCG -
added new scripts
-build_midas_db.py
allows users to build their own reference database
-call_consensus.py
calls consensus alleles at core-genomic sites
enables construction of inter-sample phylogenetic trees
-compare_genes.py
quantify inter-sample differences in gene content
-snp_diversity.py
quantify intra and inter-sample population diversity -
updated documentation