Speed up alignment if the FASTQ is pre-sorted by the read bases

[nh13]

In this case, we would obtain the same alignments, so just re-use it.

You can sort the FASTQ ahead of time via:

 gunzip -c unsorted.fastq.gz | paste - - - - | sort -t $'\t' -k 2 | tr "\t" "\n" | pigz -c > sorted.fastq.gz"

It would be better if there was a tool for this.