fastqutils / merge

Merges two (or more) paired end FASTQ files together for combined mapping.
The files need to have the paired reads in the same order. They will be
written out as:

@name1
seq1
+
qual1
@name1
seq2
+
qual2
...

The merged file is written to stdout.

Usage: fastqutils merge {-slash} file1.fastq{.gz} file2.fastq{.gz} ...

-slash    Split the read name at a '/' (Illumina paired format)