2015-03-27 01:54:43 +01:00
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Cutadapt: trim adapters from high-throughput sequencing reads
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Cutadapt finds and removes adapter sequences, primers, poly-A tails
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and other types of unwanted sequence from your high-throughput
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sequencing reads.
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Cleaning your data in this way is often required: Reads from small-RNA
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2016-11-14 21:50:57 +01:00
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sequencing contain the 3' sequencing adapter because the read is
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2015-03-27 01:54:43 +01:00
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longer than the molecule that is sequenced. Amplicon reads start with
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a primer sequence. Poly-A tails are useful for pulling out RNA from
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2016-11-14 21:50:57 +01:00
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your sample, but often you don't want them to be in your reads.
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2015-03-27 01:54:43 +01:00
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Cutadapt helps with these trimming tasks by finding the adapter or
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primer sequences in an error-tolerant way. It can also modify and
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filter reads in various ways. Adapter sequences can contain IUPAC
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wildcard characters. Also, paired-end reads and even colorspace data
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is supported. If you want, you can also just demultiplex your input
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data, without removing adapter sequences at all.
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Cutadapt comes with an extensive suite of automated tests and is
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available under the terms of the MIT license.
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If you use cutadapt, please cite:
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Marcel Martin. Cutadapt removes adapter sequences from high-throughput
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sequencing reads. EMBnet.journal, 17(1):10-12, May 2011. DOI:
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http://dx.doi.org/10.14806/ej.17.1.200
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