tools to support genome and metagenome analysis
Project description
genome-grist - map Illumina metagenomes to GenBank genomes
(1) download a metagenome
(2) process it into trimmed reads, and make a sourmash signature
(3) search the sourmash signature with 'gather' against sourmash databases, e.g. all of genbank
(4) download the matching genomes from genbank
(5) map all metagenome reads to genomes using minimap - map_reads and extract_mapped_reads
(6) extract matching reads iteratively based on gather, successively eliminating reads that matched to previous gather matches - extract_gather
(7) run mapping on “leftover” reads to genomes - map_gather
(8) summarize all mapping results for comparison and graphing - summarize_gather
Why the name grist?
In the sourmash family of names (sourmash, wort, distillerycats, etc.)
NOT: https://en.wikipedia.org/wiki/Grist_(computing)
THIS: https://en.wikipedia.org/wiki/Grist
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