Read interleaved reads [feature request]

[sjackman]

I'd like to be able to read interleaved reads with NxTrim. Even better if it implements a smart pairing feature similar to bwa mem -p that allows for occasional unpaired reads (but not strictly necessary). Also awesome if it can read from standard input: e.g.

fastq-dump -Z --split-spot SRR3663860 \
  | nxtrim --stdout --justmp --joinreads --rf --preserve-mp /dev/stdin \
  | bwa mem -p ref.fa /dev/stdin \
  | samtools sort -o foo.bam /dev/stdin

[sjackman]

If the interleaved file is on disk, this work around works. It doesn't work though when streaming, as above.

nxtrim --stdout --justmp --rf \
    -1 <(seqtk seq -1 dmelanogaster.mp.fq.gz) \
    -2 <(seqtk seq -2 dmelanogaster.mp.fq.gz) \

[jaredo]

I was just going to suggest seqtk as a workaround. I will try to make some time for this (although probably not the smart pairing).

FYI I have never seen much improvement with --joinreads and tend to leave it off for simplicity's sake.

[sjackman]

Thanks!