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alexmsalmeida / metamap

Snakemake workflow to map and quantify microbial genomes in metagenomic reads
MIT License
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reference fasta #2

Open metalichen opened 1 year ago

metalichen commented 1 year ago

Hi there! Thanks for the pipeline, it looks like exactly what I needed for my analysis.

Quick question - do I understand it correctly that if I have my reference genomes each in multiple contigs, I need to run the pipeline separately for each reference? Or can I run it on multiple genome at once? Thanks!

alexmsalmeida commented 1 year ago

Hi @metalichen,

If you have a multi-FASTA per genome, you should combine them all into one file and use that as your reference. To make sure the workflow knows which contig belongs to which genome make sure the names of the contigs in the final FASTA file are structured as [genome_name]_1, [genome_name]_2, etc.

metalichen commented 1 year ago

Thank you! This worked perfectly