Version 0.1

Small tool to simulate AdapterContamination of NGS reads.

Usage:

java -jar AdapterContaminator.jar input.fq 75 "AGGGAAATT"

adds randomly adapter fragments of length n = $size("AGGGAAATT") to your sequencing reads, replacing n bases with adapter sequence. Output is written to a input.fq.ACcont.fq file, which can then be processed with your adapter clipping tool.

Current version can only simulate perfect adapters of variable size, we might include sequencing erors to adapter sequences in upcoming versions, too.

If you specify a desired library size longer than what you have as read length in the simulated ART FastQ file, the adapter will be used to fill up your read. In this case you might see longer adapter fragments than in the case where you simply sequenced "to saturation" of your library size.