Comments (4)
Sounds good to me!
from taxprofiler.
Ok. I'll implement it in that way.
from taxprofiler.
My preliminary idea is that maybe the long read host removal should be in its own subworkflow
(name suggestion: LONGREAD_HOSTREMOVAL
) and run after LONGREAD_PREPROCESSING
subworkflow:
- create minimap2 index
- align long reads using the index to the reference; get bam as output
- get all unmapped reads from bam output using
samtools view -f 4
@jfy133 Does this sound like an ok preliminary plan?
from taxprofiler.
Make sure to make minimap2 index generation is optional, as with short-reads
from taxprofiler.
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