Optimizing assembly of (very) large metagenomes

[clb21565]

Dear OPERA-MS creators,

Thanks for the great tool!

I am attempting to assemble a very large and complex metagenome (~5e9 150 bp PE reads or ~ 8e11 basepairs short reads) with about 16 gbs of nanopore reads. I am noticing the read pre-processing with BWA is taking quite a bit of time:

[M::main_mem] read 1544278 sequences (200000192 bp)...
[M::mem_process_seqs] Processed 1544278 reads in 429.336 CPU sec, 21.544 real sec

At this rate (~1.5 million reads per ~20 seconds) it would take a very long time to finish this just this task. Would you mind providing guidance on whether or not this is even possible with OPERA-MS? And, if so, how could one go about optimizing the process?

Thank you again.

Cheers,

Connor

[nnnagara]

Dear Connor, We have indeed assembled datasets of this size though I will let Denis and Chengxuan comment on the runtime, Regards, Niranjan From: Connor Brown <notifications@github.com> Reply-To: CSB5/OPERA-MS <reply@reply.github.com> Date: Saturday, 20 February 2021 at 2:02 AM To: CSB5/OPERA-MS <OPERA-MS@noreply.github.com> Cc: Subscribed <subscribed@noreply.github.com> Subject: [CSB5/OPERA-MS] Optimizing assembly of (very) large metagenomes (#53) Dear OPERA-MS creators, Thanks for the great tool! I am attempting to assemble a very large and complex metagenome (~5e10 150 bp PE reads or ~ 7e11 basepairs short reads) with about 16 gbs of nanopore reads. I am noticing the read pre-processing with BWA is taking quite a bit of time: [M::main_mem] read 1544278 sequences (200000192 bp)... [M::mem_process_seqs] Processed 1544278 reads in 429.336 CPU sec, 21.544 real sec At this rate (~1.5 million reads per ~20 seconds) it would take a very long time to finish this task. Would you mind providing guidance on whether or not this is even possible with OPERA-MS? And, if so, how could one go about accomplishing it? Thank you again. Cheers, Connor — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#53>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACNYPUAQ5GL7MNLO2AD2Q3TS72RS3ANCNFSM4X4ZGZDQ>. This e-mail and any attachments are only for the use of the intended recipient and may contain material that is confidential, privileged and/or protected by the Official Secrets Act. If you are not the intended recipient, please delete it or notify the sender immediately. Please do not copy or use it for any purpose or disclose the contents to any other person.