take interleaved files, perhaps on stdin

[macmanes]

ENHANCEMENT:

I'd like to be able to use kallisto as such:

seqtk mergepe read1.fq read2.fq | skewer | kallisto quant -i -

basically, moving from raw reads, through adapter trimming, to kallisto streaming, without the need to write intermediate files.. Any change of getting this supported?

[ewallace]

I would also really like this.

[huipan1973]

Me too.