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Arcadia-Science / metagenomics

A Nextflow workflow for QC, evaluation, and profiling of metagenomic samples using short- and long-read technologies
MIT License
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Time-series reciprocal mapping #20

Open elizabethmcd opened 1 year ago

elizabethmcd commented 1 year ago

Current mapping functionality only maps 1:1 for sample reads:assembly, with a time-series want to reciprocally map to all samples to get differential coverage information

elizabethmcd commented 1 year ago

--time-series flag for reciprocal mapping for differential coverage/abundance, and summary plots that show this information. This will have to be tested with a different test profile conf and dataset that is actually part of a time series to make sure everything is working

elizabethmcd commented 1 year ago

Make a mapping flag either --mapping self or --mapping reciprocal with the self option as default to only do 1:1 mapping for corresponding reads:assemblies, whereas reciprocal will be for time-series all-v-all