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Atropos finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
Cleaning your data in this way is often required: Reads from small-RNA sequencing contain the 3’ sequencing adapter because the read is longer than the molecule that is sequenced. Amplicon reads start with a primer sequence. Poly-A tails are useful for pulling out RNA from your sample, but often you don’t want them to be in your reads.
Atropos helps with these trimming tasks by finding the adapter or primer sequences in an error-tolerant way. It can also modify and filter reads in various ways. Adapter sequences can contain IUPAC wildcard characters. Also, paired-end reads and even colorspace data is supported. If you want, you can also just demultiplex your input data, without removing adapter sequences at all.
Atropos is a fork of the venerable Cutadapt (http://cutadapt.readthedocs.io) NGS read-trimmer. Atropos improves upon Cutadapt by adding multi-threading support and several other nice features.
The parts of Atropos that were carried over from Cutadapt are under an MIT license, while improvements and additions are in the public domain.
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