Hi James, another question/comments regarding host...
# magr
Ruiqi Li
03/09/2026, 6:05 AMHi James, another question/comments regarding host reads removal:
Ruiqi Li
03/09/2026, 6:06 AMsince there is one genome available in Osedax, I used genome fasta from that species for all samples, which are from multiple species
Ruiqi Li
03/09/2026, 6:06 AM Copy code
--host_fasta /project2/ckenkel_26/liruiqi/Osedax_meta/Osedax_frankpressi.fna
--host_removal_verysensitiveRuiqi Li
03/09/2026, 6:07 AMIt is pretty effective for the same species
Ruiqi Li
03/09/2026, 6:08 AMbut hardly removed any sequence for other species
Ruiqi Li
03/09/2026, 6:10 AMWould you mind confirming that I am using the parameters correctly? Is the removing host reads step only for reducing run time for assemblers? If so, since resources is not a concern, I guess I can run mag pipeline with the host reads, and just remove their contigs after the pipeline is done? Thanks for your insights!
j
Jim Downie
03/09/2026, 8:28 AMIt seems likely that your species are too divergent from the genome you have to get good mapping rates. You could try modifying the bowtie2 parameters, though I wouldn’t know what to suggest you change, or alternatively if your data is small enough you could skip host removal altogether -assembly will take longer and require more resources, but if you have them you will still be able to assemble the symbionts.
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r
Ruiqi Li
03/09/2026, 3:26 PMThank you!
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