What it does

Splits a single fastq dataset representing paired-end run into two datasets (one for each end). This tool works only for datasets where both ends have the same length.

Sequence identifiers will have /1 or /2 appended for the split forward and reverse reads, respectively.

Input format

A multiple-fastq file, for example:

@HWI-EAS91_1_30788AAXX:7:21:1542:1758
GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
+HWI-EAS91_1_30788AAXX:7:21:1542:1758
hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR

Outputs

Forward Read:

@HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC
+HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh

Reverse Read:

@HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
+HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR