cutadapt 1.16

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; and poly-A tails are useful for pulling out RNA from your sample, but typically you don’t want them to be in your reads.
Cutadapt helps with these trimming tasks by finding the adapters or primers in an error-tolerant way. It can also filter reads by length and do quality trimming. 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.

Accessing the software

To load the module:

$ module load cutadapt/1.16-iomkl-2018a-Python-3.6.3

An example command to include in your job script:

$ cutadapt -a AACCGGTT -o output.fastq.gz input.fastq.gz

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

Previous versions of this application are recorded below:

At present there are no previous versions of this application on the BlueBEAR service.

Known Problems & Limitations


Other Information

The Support Level for this application is An.

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Last modified: 15 August 2018