Support for flipping reads based on primer direction #196
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Could speed up the FASTQ reverse complement (avoid SeqRecord), but more elegant to make two calls to cutadapt?
This avoids the possibility of a read pair being counted twice (if it managed to give primer matches in either orientation). Note first call to cutadapt is given FASTQ, while the second gets FASTA - don't think lack of quality scores matters here.
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With some library preparations, expect about 50% of the reads to be inverted - so this can make a big difference to the apparent yield.
This is hopefully a short-term implementation by calling cutadapt twice, there are open issues for enhancing cutadapt to do this itself:
marcelm/cutadapt#220
marcelm/cutadapt#402