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AlignTips and genome size #252
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There is a fix in v2.1 to reduce the number of reads recruited for the winnowmap alignment step which speeds it up significantly on genomes with very homozygous or heterozygous genomes (essentially those where the initial graph had large nodes from the 1-buildGraph step). Depending on what your graph looks like in that step, this could also help your runtime. |
Super, thanks for the quick feedback. So the alignTipsONT process took ~36 min and used ~66G with I dont think the runtime of this step is excessive when the I just checked and the following meryl command took took 21 min and 3.5G memory on the 28G tips.fasta.
On the other hand, the following winnowmap command with kmers included took 42 min and 68G memory with 24 threads:
Strangely, running it without the kmers was actually much faster?
So yeah, totally not worth it to do the kmer counting step. |
Do you have a custom version of winnowmap? As far as I see from this issue (marbl/Winnowmap#40) it doesn't support the index size parameter and when I provide the -I flag it doesn't run. |
Yes I was also confused by that issue. In practice, the |
I'm running winnowmap (from verkko conda env) without the This is the content of the tips.fasta file:
This is the command, now without the
This is the output so far. Note the
So the confusing things relative to that thread are:
|
I confirmed that adjusting the -I makes a huge performance difference (something like 10x speedup) on genomes > 4gb. I do see slight differences in the alignments but mostly it seems that duplicates are removed that were present before. It seems the -I flag was removed post the 2.0.3 release so I'm going to confirm that it is expected to work OK without a saved index and then update verkko. |
Wow, that's bizarre. And yeah, not only is it faster but without it, all the mapQs and supplementary/secondary flags will be totally wrong when aligning to genomes >4G. |
… speeds up mappings to genomes >4gb (#252)
I've done tests on a couple of genomes and it not only maps much faster but also improves the assembly, thanks for pointing this out. |
Hello,
I have a few questions regarding the Verkko and the alignTips step:
-I
flag locally to-I 40G
, but it would be nice if it were set by default to a larger value or at least there was a command line option in Verkko to adjust it.Thanks a lot in advance for the clarifications!
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