Tools to remove adapter sequences from next-generation sequencing data

List of various tools to detect and trim adapter sequences from sequencing data.

Cutadapt
Cutadapt removes adapter sequences from high-throughput sequencing data. This is usually necessary when the read length of the sequencing machine is longer than the molecule that is sequenced, for example when sequencing microRNAs.

FAR – The Flexible Adapter Remover
FAR removes adapter sequences from deep sequencing data in FASTA/Q, CSFASTA/Q format (Illumina / Roche 454 / SOLiD Colorspace). It also demultiplexes barcoded runs.

Adapterremoval
This program was developed to remove residual adapter sequences from next generation sequencing reads. The program handles both single end and paired end data.

ea-utils
Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline – but should work with any FASTQs.

Biopiece: remove_adaptor
Locates and removes a specified adaptor sequence from sequences in stream.

FASTQ/A Clipper
Removing sequencing adapters / linkers, part of FASTX tool kit.

Removing sequencing adapters
This is some example code for the removal of sequencing adapters from next generation sequence reads. This is useful for cleaning up sequence from Solexa/Illumina GA machines, and may also be relevant for the removal of adapter/primer sequence from other types of sequence machine.

Trimmomatic: A flexible read trimming tool for Illumina NGS data
Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.

PRINSEQ
Trim sequences to a certain length, trim poly-A/T tails, trim low quality ends, trim bases from the ends.

TagCleaner

The TagCleaner tool can be used to automatically detect and efficiently remove tag sequences (e.g. WTA tags) from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface.

ClipReadsWalker
This tool provides simple, powerful read clipping capabilities to remove low quality strings of bases, sections of reads, and reads containing user-provided sequences.

Adaptor trimming script from mirTools
Perl script used to filter low quality short reads, remove polyA, trim 3′/5′ adapter and generate the the proper input format of mirTools.

If you know other tools to trim adapter sequences, please feel free to write in comments.

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