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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
The text was updated successfully, but these errors were encountered:
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.
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.
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
The text was updated successfully, but these errors were encountered: