I just discovered that with oatk/mitohifi it should be possible to assemble mitochondria (and chloroplasts) instead of only identifying them in an assembly. I will do some testing to see how to connect this into the currently assembly model while retaining the modularity of assembler choice. There are two options to investigate:
- do
oatk/mitohifi assembly in parallel to full genome assembly and then after that filter contigs
- do
oatk/mitohifi assembly first, then filter reads, then do nuclear genome assembly
Some practical notes to future self:
oatk can be installed through bioconda but mitohifi needs to be run via apptainer.- I did a very quick test with some A. thaliana data and it seems
oatk on the input hifi reads is not significantly faster to run that oatk on a resulting hifiasm assembly; meaning that probably we only need to investigate the former.
I just discovered that with
oatk/mitohifiit should be possible to assemble mitochondria (and chloroplasts) instead of only identifying them in an assembly. I will do some testing to see how to connect this into the currently assembly model while retaining the modularity of assembler choice. There are two options to investigate:oatk/mitohifiassembly in parallel to full genome assembly and then after that filter contigsoatk/mitohifiassembly first, then filter reads, then do nuclear genome assemblySome practical notes to future self:
oatkcan be installed through bioconda butmitohifineeds to be run via apptainer.oatkon the input hifi reads is not significantly faster to run thatoatkon a resultinghifiasmassembly; meaning that probably we only need to investigate the former.