Adding Metagenomics assemblers and YEAT assembler Metagenomics assembler options

bioforensics / yeat

YEAT: Your Everyday Assembly Tool

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Adding Metagenomics assemblers and YEAT assembler Metagenomics assembler options #39

Closed danejo3 closed 10 months ago

danejo3 commented 1 year ago

Another aspect of genome assembly is meta genomic assembly.

To assemble meta samples, a few popular assemblers have some kind of --meta flag to enable Metagenomics assembly.

For examples,

spades has the --meta flag.
Flye has the --meta flag as well.
A forked repo from hifiasm has a Metagenomics assembler called hifiasm-meta.

Next steps for YEAT is to add this capability.

danejo3 commented 10 months ago

Users will continue to use the extra_args params in the config to enable Metagenomics assembly for spades and flye. Hifiasm-meta assembly algorithm was integrated in #49 .