How to cite Cutadapt?

It is currently being developed within NBIS (National Bioinformatics Infrastructure Sweden). If you use Cutadapt, please cite DOI:10.14806/ej.

How does Cutadapt work?

Cutadapt searches for the adapter in all reads and removes it when it finds it. Unless you use a filtering option, all reads that were present in the input file will also be present in the output file, some of them trimmed, some of them not. Even reads that were trimmed to a length of zero are output.

What is adapter trimming?

Illumina FASTQ file generation pipelines include an adapter trimming option for the removal of adapter sequences from the 3′ ends of reads. Adapter sequences should be removed from reads because they interfere with downstream analyses, such as alignment of reads to a reference.

What can I use cutadapt for in IUPAC?

Cutadapt helps with these trimming tasks by finding the adapter or primer sequences in an error-tolerant way. It can also modify and filter single-end and paired-end reads in various ways. Adapter sequences can contain IUPAC wildcard characters. Cutadapt can also demultiplex your reads. Cutadapt is available under the terms of the MIT license.

How are read modifications applied in cutadapt 3.2?

Read modification options are applied. This includes adapter removal , quality trimming, read name modifications etc. The order in which they are applied is the order in which they are listed in the help shown by cutadapt –help under the “Additional read modifications” heading.

How to use cutadapt as a command line tool?

As an easy to use alternative, we developed the command-line tool cutadapt, which supports 454, Illumina and SOLiD (color space) data, offers two adapter trimming algorithms, and has other useful features. Cutadapt, including its MIT-licensed source code, is available for download at http://code.google.com/p/cutadapt/

Which is the output file format for cutadapt?

The supported input and output file formats are FASTA and FASTQ, with optional compression. The input file format is recognized from the file name extension. If the extension was not recognized or when Cutadapt reads from standard input, the contents are inspected instead. The output file format is also recognized from the file name extension.