What it does

The trim_adapters utility is based on a script by Jason Buenrostro. Instead of looking for known adapter sequence, it aligns paired reads to each other and trims off sequence outside the alignment. More precisely, it searches the forward read for the reverse complement of a specified number of bases (20 by default) at the beginning of the reverse read, then falls back to finding the best alignment of the two reads, using the minimum Levenshtein distance between them.

Input

It requires 2 inputs: The (optionally gzipped) FASTQ file containing the forward reads and the (optionally gzipped) FASTQ file containing the reverse reads.

Output

Generates 2 gzipped fastq files with adapters trimmed.