tools to support genome and metagenome analysis
Project description
genome-grist - map Illumina metagenomes to GenBank genomes
- download a metagenome
- process it into trimmed reads, and make a sourmash signature
- search the sourmash signature with 'gather' against sourmash databases, e.g. all of genbank
- download the matching genomes from genbank
- map all metagenome reads to genomes using minimap -
map_readsandextract_mapped_reads - extract matching reads iteratively based on gather, successively eliminating reads that matched to previous gather matches -
extract_gather - run mapping on “leftover” reads to genomes -
map_gather - 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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