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multithreaded or single thread? #7
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Hi there, If you are using minimap2 as your aligner, If one is using nucmer, that cannot be multithreaded. Please reopen if you have any additional questions. Thanks, |
Hi Micheal, I have a couple of follow up questions. I tried to use multiple threads in my ragtag run - this is the command I used - I am trying to scaffold a maize assembly, but am constrained by low coverage. My assembly has a large number of small contigs, lot of them less than 1000bp and as noted in the reply to this question -malonge/RaGOO#53 I have sections like this - 500bp contigs spaced out, but these are not considered during scaffolding in Ragoo. Example from the short read assembly aligned to B73 maize reference genome. |
Hi there, With regards to the Second, the
With regards to the mapping of shorter contigs, this is substantially improved in RagTag relative to RaGOO. First of all, by default, all unique alignments are kept regardless of their length. Secondly, you can adjust the Just to speculate, there may be a relatively small number of short unique alignments since it looks like you are scaffolding a maize genome, which is highly repetitive. Let me know if you have trouble and I can help you adjust parameters. In my experience, minimap2 works fine for most assemblies, though you may consider trying nucmer here just incase (though it will be quite slow). Thanks |
I am facing a similar task - scaffolding a plant assembly with low contiguity (~5k N50). I was wondering if there were any conclusions about how this should be done. Any tips other than decreasing |
Hi @soungalo, If I really need to tune the alignments, I personally use Nucmer since I find it easier to interpret the results. Using the |
I am going to close this for now but please reopen if anything comes up. |
Hi,
I have a quick question - does RagTag support multiple threads to speed up the processing? or is it single-threaded?
If it does have support for multi-threaded ops - what is the flag to enable it? same as Ragoo?
Thanks!
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