What's the benefit of using the `no_alt_analysis_set` Bowtie2 index over the primary assembly?

Question

[O.rka]

Bowtie2 has preconfigured indexes:

GRCh38 no alt analysis https://genome-idx.s3.amazonaws.com/bt/GRCh38_noalt_as.zip

Telmore-2-Telomore https://genome-idx.s3.amazonaws.com/bt/chm13v2.0.zip

What's the benefit of using the GRCh38 no alt analysis?

I'm using the human genome solely as a reference to map to while removing human contamination from metagenomics.

[ATpoint]

To be clear, the T2T is a new reference genome, it's not GRCh38. https://www.science.org/doi/10.1126/science.abj6987

Answer 1

[Carambakaracho]

In 2017 Heng Li posted something worth reading on which reference genome (GRCh37/38) to use:

https://lh3.github.io/2017/11/13/which-human-reference-genome-to-use

In your use case, I would use the T2T assembly CHM13v2.0 - you get the complete genome and don't have to worry about additional knowledgebases that use a different reference like GRCh38 or 37.