Is there any reason to discard singletons after de-hosting metagenomic reads?
I an double de hosting metagenomic reads and am wondering if there is any reason to discard singletons after both alignment steps? The workflow is as:
- Map to host 1
- Convert to fastq and repair.sh to resort
- Map to host 2
- Convert to fastq and repair.sh to resort
- Assemble
During steps 2 and 4 I believe the default behaviour of repair.sh is to discard singletons but I have the option to output them separately. Is there any reason not to recombine the singletons with the origin fastq file before assembly (step 5)?
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robert.murphy •
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