Checkpoint Large Metagenome Assembly

[mbcouger]

Hello,

I am running a very large assembly on a supercomputer that has a local disk to page off of. Is there any way I can tell megahit to stop after a certain kmer point (or if I told it only to do one kmer can I modify it to work this way) so I can copy the current checkpoint back to a non volatile disk.

Many Thanks! Brian

[mbcouger]

Hello Voutcn,

I went back and looked through my logs for previous metageomes assemblies and realized that I can run the core commands individually. If possible, do you have preferred quality trimming protocol to remove erroneous kmers.

Many Thanks, Brian

[voutcn]

You can use --continue to resume a job.

For quality trimming/filtering I don't have personal suggestions. There are some workshop materials you can refer to, for example https://usda-ars-gbru.github.io/Microbiome-workshop/tutorials/metagenomics/ https://2017-dibsi-metagenomics.readthedocs.io/en/latest/quality.html

[mbcouger]

Thanks Voutcn!