AdapterRemoval searches for and trims remnant adapter sequences from High-Throughput Sequencing (HTS) data, trims low quality bases, merges overlapping paired-ended reads, and generates QC reports (human and machine readable). AdapterRemoval can additionally demultiplex sequencing reads and can construct a consensus adapter sequence from paired-ended reads.

See the Getting started and Example usage pages to get started processing your own data. See the Detailed overview page for a description of processing carried out by AdapterRemoval and the options affecting each step of the process. See the Input and output page for details on the input files read by AdapterRemoval and resulting output filess. And finally, see the Migrating from older version page if you are upgrading from an older version of AdapterRemoval.

If you use AdapterRemoval v3, then please cite the paper:

Schubert, Lindgreen, and Orlando (2016). AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Research Notes, 12;9(1):88

AdapterRemoval was originally published in Lindgreen 2012:

Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation Sequencing Reads, BMC Research Notes, 5:337

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