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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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Support for highly accurate long reads? #721

Closed MrTomRod closed 2 months ago

MrTomRod commented 3 months ago

Dear ATLAS team

We really like your pipeline and have used it for short-read metagenome datasets.

For highly accurate long reads, it seems to us that different assemblers and binners might be necessary.

Are you planning to support such input data in the future? If not, how would you process such data? Maybe use something like metaMDBG, a metagenome-aware assembler plus your suite of quality checks?

Best, MrTomRod

SilasK commented 3 months ago

Hey @MrTomRod, In theory I would like Atlas to support long reads (other than hybrid assembly). But then I don't have the incentive to work on that, as I don't have data myself.

@jmtsuji made and extension of Atlas for ONT.

One option would be simply to use meta-flye as assembler for long-reads only. but as you point out there are more and more data types coming in that don't seem to need binning or that can be assembled directly into MAGs.