tools to support genome and metagenome analysis
Project description
genome-grist - map Illumina metagenomes to GenBank genomes
In brief
genome-grist
is a toolkit to do the following:
- 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
- extract matching reads iteratively based on gather, successively eliminating reads that matched to previous gather matches
- run mapping on “leftover” reads to genomes
- summarize all mapping results
Installation
The command:
python -m pip install genome-grist
will install the latest version. Plase use python3.7 or later. We suggest using an isolated conda environment.
Quick start:
Run the following three commands.
First, download SRA sample HSMA33MX, trim reads, and build a sourmash signature:
genome-grist process HSMA33MX smash_reads
Next, run sourmash signature against genbank:
genome-grist process HSMA33MX smash_reads
(NOTE, this depends on the latest genbank genomes and won't work for most people just yet; for now, use cached results from the repo:
cp tests/test-data/HSMA33MX.x.genbank.gather.csv outputs/genbank/
touch outputs/genbank/HSMA33MX.x.genbank.gather.out
)
Finally, download the reference genomes, map reads and produce a summary report:
genome-grist process HSMA33MX summarize -j 8
Full set of top-level process
targets
- download_reads
- trim_reads
- smash_reads
- gather_genbank
- download_matching_genomes
- map_reads
- summarize
Support
genome-grist is alpha-level software. Please be patient and kind :).
Please ask questions and add comments by filing github issues.
Why the name grist
?
'grist' is in the sourmash family of names (sourmash, wort, distillerycats, etc.) See Grist.
(It is not the computing grist!)
CTB Nov 7, 2020
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