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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
The text was updated successfully, but these errors were encountered:
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 <[email protected]>
Reply-To: CSB5/OPERA-MS <[email protected]>
Date: Saturday, 20 February 2021 at 2:02 AM
To: CSB5/OPERA-MS <[email protected]>
Cc: Subscribed <[email protected]>
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
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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
The text was updated successfully, but these errors were encountered: