output interleaved fastQ format?

relipmoc / skewer

MIT License

95 stars 17 forks source link

output interleaved fastQ format? #21

Open macmanes opened 9 years ago

macmanes commented 9 years ago

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

standage commented 8 years ago

Support for interleaved fastq input would be great as well.

andreas-wilm commented 6 years ago

👍