Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

add action for estimating (relative) abundances MAGs/MAG-based taxonomic profiles #33

Closed
nbokulich opened this issue Apr 14, 2023 · 1 comment
Assignees
Labels
enhancement New feature or request

Comments

@nbokulich
Copy link
Contributor

When performing taxonomic profiling of MAGs, abundance information currently is not preserved. This is needed to then estimate the (relative) abundances of MAGs/taxa.

This can be done in a few steps:

  1. map reads to MAGs.
  2. normalize by genome length, e.g., calculate RPKM or similar. c.f., bracken uses genome length to calculate relative abundances of taxa when doing read-based profiling.

This action should probably be independent to taxonomic classification, i.e., to output a feature table of MAG abundances per sample.

Some useful reading

  1. Challenges in benchmarking metagenomic profilers describes the differences between sequence abundance and taxon abundance for estimating relative abundances in metagenomes.
  2. mOTUs2 uses a single-copy marker-gene approach for accurately estimating taxonomic abundance from reads, but gives a good overview of the different approaches and a comparison vs. MAGs.
@misialq
Copy link
Contributor

misialq commented Nov 7, 2024

Closed by #177

@misialq misialq closed this as completed Nov 7, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

No branches or pull requests

2 participants