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metagenome-atlas / atlas

ATLAS - Three commands to start analyzing your metagenome data
https://metagenome-atlas.github.io/
BSD 3-Clause "New" or "Revised" License
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How to make an rarefaction curve based on single copy genes #163

Closed SilasK closed 3 years ago

SilasK commented 5 years ago

1. Cluster gene catalog with high sensitivity on nucleotide level

Change config file:

genecatalog:
  clustermethod: cd-hit-est 
  minlength_nt: 100
  minid: 0.98
  coverage: 0.9
  extra: ""

2. Run atlas genecatalog

atlas assemble config.yaml genecatalog

(Atlas v2.1 atlas run genecatalog )

This clusters the genes, calculate the abundance of genes output can be found in Genecatalog/counts and claissify single copy genes. output:

atlas assemble Genecatalog/annotation/single_copy_genes_bacteria.tsv atlas assemble Genecatalog/annotation/single_copy_genes_archaea.tsv

This is done with diamond, based on a databased shiped with DASTool, see it's article for more info. There are defenetly better ways to do it, e.g. BUSCOs