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metagenome_contigs #9

Closed wisnu-adi closed 3 years ago

wisnu-adi commented 3 years ago

Hi there,

Thank you for the awesome tool. I am analysing my shotgun metagenome dataset and have a couple of questions?

  1. As I constructed metagenome assembled genomes from the dataset, do you have a recommendation of which MAGs that I should use for BiG-MAP regarding to quality and completeness (HG MAG - 90% with less than 5% contaminants or medium quality is acceptable?)
  2. Can we use metagenome contigs instead of genome as an input for big-map?

Best wishes

Wisnu

ShailNair commented 3 years ago

@wisnu-adi BiG-MAP uses the output of anti- or gutSMASH analysis to cluster BCGs. So, its better to check anti- or gutSMASH repositories for your query.

In general, the Lower the completeness lower are the chances to get a complete set of genes. Higher the contamination, the higher the chances of dubious results. Currently, any bin with at least 70% completion and less than 10% contamination (but not limited to) is considered for downstream analysis as a MAG.

You can use metagenome contigs in anti- or gutSMASH and feed the output in BiG-MAP.