When trimming in paired end mode, should be able to output to an interleaved fastq. This would enable streaming output to the STDOUT (e.g., -1) when using PE reads.
Imagine combining skewer with khmer like this:
skewer -m pe | normalize-by-median.py | trim-low-abund.py
When trimming in paired end mode, should be able to output to an interleaved fastq. This would enable streaming output to the STDOUT (e.g.,
-1
) when using PE reads.Imagine combining skewer with khmer like this:
skewer -m pe | normalize-by-median.py | trim-low-abund.py