mirror of
https://github.com/Ponce/slackbuilds
synced 2024-11-26 22:06:35 +01:00
27 lines
1.2 KiB
Text
27 lines
1.2 KiB
Text
|
Cutadapt: trim adapters from high-throughput sequencing reads
|
|||
|
|
|
|||
|
|
Cutadapt 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.
|
|||
|
|
|
|||
|
|
Cutadapt 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.
|
|||
|
|
|
|||
|
|
Cutadapt comes with an extensive suite of automated tests and is
|
|||
|
|
available under the terms of the MIT license.
|
|||
|
|
|
|||
|
|
If you use cutadapt, please cite:
|
|||
|
|
Marcel Martin. Cutadapt removes adapter sequences from high-throughput
|
|||
|
|
sequencing reads. EMBnet.journal, 17(1):10-12, May 2011. DOI:
|
|||
|
|
http://dx.doi.org/10.14806/ej.17.1.200
|