Contaminant oligonucleotide sequences such as primers and adapters can occur in both ends of next-generation sequencing (NGS) reads. These adapter sequences have to be removed as they can hinder correct mapping of the reads and influence SNP calling and other downstream analyses.

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Trimmomatic
Desktop

Trimmomatic

Performs a variety of useful trimming tasks for illumina paired-end and single…

Performs a variety of useful trimming tasks for illumina paired-end and single ended data.

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skewer
Desktop

skewer

Implements a dynamic programming algorithm dedicated to the task of adapter…

Implements a dynamic programming algorithm dedicated to the task of adapter trimming. Skewer is specially designed for processing illumina paired-end sequences. Experiments on simulated data, real…

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Trim Galore!
Desktop

Trim Galore!

A wrapper tool around Cutadapt and FastQC to consistently apply quality and…

A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation…

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AlienTrimmer
Desktop

AlienTrimmer

Detects and removes multiple alien sequences in both ends of sequence reads.…

Detects and removes multiple alien sequences in both ends of sequence reads. Based on the decomposition of specified alien nucleotide sequences into k-mers, AlienTrimmer is able to determine whether…

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PEAT
Desktop

PEAT

A fast and highly accurate adapter-trimming algorithm, PEAT, designed…

A fast and highly accurate adapter-trimming algorithm, PEAT, designed specifically for paired-end sequencing. PEAT requires no a priori adaptor sequence, which is convenient for large-scale…

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cutadapt
Desktop

cutadapt

Finds and removes adapter sequences, primers, poly-A tails and other types of…

Finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Cutadapt helps with these trimming tasks by finding the…

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ShortRead
Desktop

ShortRead

Classes and methods for high-throughput short-read sequencing data.

Classes and methods for high-throughput short-read sequencing data.

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PRINSEQ
Desktop
Web

PRINSEQ PReprocessing and INformation of SEQuences

For easy and rapid quality control and data preprocessing of genomic and…

For easy and rapid quality control and data preprocessing of genomic and metagenomic datasets.

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FreClu
Desktop

FreClu

Efficient Frequency-based de Novo Short Read Clustering.

Efficient Frequency-based de Novo Short Read Clustering.

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NGS QC Toolkit
Desktop

NGS QC Toolkit

A toolkit for the quality control (QC) of next generation sequencing (NGS)…

A toolkit for the quality control (QC) of next generation sequencing (NGS) data. The toolkit comprises of user-friendly standalone tools for quality control of the sequence data generated using…

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NextClip
Desktop

NextClip

A tool for analysing reads from LMP libraries, generating a comprehensive…

A tool for analysing reads from LMP libraries, generating a comprehensive quality report and extracting good quality trimmed and deduplicated reads.

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Flexbar
Desktop

Flexbar

Preprocesses high-throughput sequencing data efficiently. Flexbar demultiplexes…

Preprocesses high-throughput sequencing data efficiently. Flexbar demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided. It increases read…

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NxTrim
Desktop

NxTrim

A tool that strives to discard as little sequence as possible from Illumina…

A tool that strives to discard as little sequence as possible from Illumina Nextera Mate Pair (NMP) reads. NxTrim makes full use of the sequence on both sides of the adapter site to build…

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ConDeTri
Desktop

ConDeTri

A method for content dependent read trimming for next generation sequencing…

A method for content dependent read trimming for next generation sequencing data using quality scores of each individual base. The main focus of the method is to remove sequencing errors from reads…

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Btrim
Desktop

Btrim

A fast and lightweight software to trim adapters and low quality regions in…

A fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines. It also can reliably identify barcodes and assign the…

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Kraken
Desktop

Kraken

A set of tools for quality control and analysis of high-throughput sequence…

A set of tools for quality control and analysis of high-throughput sequence data.

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SeqtrimNEXT
Desktop

SeqtrimNEXT

A customizable and distributed pre-processing software for NGS (Next Generation…

A customizable and distributed pre-processing software for NGS (Next Generation Sequencing) biological data.

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TagCleaner
Desktop

TagCleaner

The tool can be used to automatically detect and efficiently remove tag…

The tool can be used to automatically detect and efficiently remove tag sequences (e.g. WTA tags) from genomic and metagenomic datasets.

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ERNE
Desktop

ERNE Extended Randomized Numerical alignEr

A short string alignment package whose goal is to provide an all-inclusive set…

A short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads. ERNE 2 (a.k.a. bw-erne) uses the Burrows Wheeler Transformation (BWT) to…

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AdapterRemoval
Desktop

AdapterRemoval

A comprehensive tool for analyzing next-generation sequencing data.…

A comprehensive tool for analyzing next-generation sequencing data. AdapterRemoval is able to pre-process both single and paired-end data. The program locates and removes adapter residues from the…

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TagDust
Desktop

TagDust

Eliminates artifactual reads from next-generation sequencing data sets.…

Eliminates artifactual reads from next-generation sequencing data sets. TagDust2 extracts more reads of higher quality compared to other approaches. Processing of multiplexed single, paired end and…

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leeHom
Desktop

leeHom

Removes the adaptors and reconstructs the original DNA sequences using a…

Removes the adaptors and reconstructs the original DNA sequences using a Bayesian maximum a posteriori probability approach. leeHom is faster, and provides a more accurate reconstruction of the…

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DNApi
Desktop

DNApi De Novo Adapter prediction iterative algorithm

Predicts the 3´ adapter sequence de novo and provides the user with cleansed…

Predicts the 3´ adapter sequence de novo and provides the user with cleansed small RNA sequences ready for down stream analysis. DNApi has been tested on 539 publicly available small RNA libraries…

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Figaro
Desktop

Figaro

Identifies and removes the vector from raw DNA sequence data without prior…

Identifies and removes the vector from raw DNA sequence data without prior knowledge of the vector sequence. Figaro is able to determine which DNA words are most likely associated with vector…

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Seqpurge
Desktop

Seqpurge

A highly-sensitive adapter trimmer that uses a probabilistic approach to detect…

A highly-sensitive adapter trimmer that uses a probabilistic approach to detect the overlap between forward and reverse reads of Illumina sequencing data. SeqPurge can detect very short adapter…

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ADEPT
Desktop

ADEPT A Dynamic Error-detection Program with Trimming

Dynamically assesses errors within reads based on position-specific and local…

Dynamically assesses errors within reads based on position-specific and local quality scores. ADEPT is the first tool that we are aware of that dynamically processes data and relies on within-dataset…

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QTrim
Desktop
Web

QTrim

A package for the quality trimming of high throughput sequencing data. QTrim is…

A package for the quality trimming of high throughput sequencing data. QTrim is an averaging approach for the quality trimming of Roche/454 sequence reads. It is implemented both as an executable…

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CANGS
Desktop

CANGS Cleaning and Analyzing Next Generation Sequences

A flexible and user-friendly integrated software utility: CANGS is designed for…

A flexible and user-friendly integrated software utility: CANGS is designed for amplicon based biodiversity surveys using the 454 sequencing platform. CANGS filters low quality sequences, removes PCR…

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Lucy
Desktop

Lucy

Provides a raw DNA sequence trimming and visualization tool. Lucy allows users…

Provides a raw DNA sequence trimming and visualization tool. Lucy allows users to change parameters, trim multiple sequences and visualize the results within an integrated, easy-to-use graphical user…

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RepeatSoaker
Desktop

RepeatSoaker

Removes reads overlapping low-complexity (repeat) regions from aligned…

Removes reads overlapping low-complexity (repeat) regions from aligned sequencing data. RepeatSoaker helps to emphasize the biological signals within the data, reflected by more significant p-values…

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UrQt
Desktop

UrQt

A quality control method for unsupervised quality trimming of next generation…

A quality control method for unsupervised quality trimming of next generation sequencing reads. By finding the best segmentation to delimit a segment of good quality nucleotides, UrQt greatly…

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QcReads
Desktop

QcReads

Provides an efficient tool for trimming adapter sequences and low quality…

Provides an efficient tool for trimming adapter sequences and low quality sequences, in raw reads generated by the high throughput sequencing platforms.

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Cookiecutter
Desktop

Cookiecutter

A computational tool for rapid read extraction or removing according to a…

A computational tool for rapid read extraction or removing according to a provided list of k-mers generated from a FASTA file. Cookiecutter is based on the implementation of the Aho-Corasik algorithm…

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ngsShoRT
Desktop

ngsShoRT next-generation sequencing Short Reads Trimmer

A flexible and comprehensive open-source software package written in Perl that…

A flexible and comprehensive open-source software package written in Perl that provides a set of algorithms commonly used for pre-processing NGS short read sequences.

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PyroTrimmer
Desktop

PyroTrimmer

Removes the barcodes, linkers, and primers, trims sequence regions with low…

Removes the barcodes, linkers, and primers, trims sequence regions with low quality scores, and filters out low-quality sequence reads. Although these functions have previously been implemented in…

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trimseq
Desktop

trimseq

Removes unwanted characters from start and end of sequence(s). trimseq is an…

Removes unwanted characters from start and end of sequence(s). trimseq is an Emboss package that reads one or more sequences and writes the same sequences out, but removing any regions at the start…

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trimest
Desktop

trimest

Removes poly-A tails from nucleotide sequences. trimest reads one or more…

Removes poly-A tails from nucleotide sequences. trimest reads one or more nucleotide sequences and writes them out again but with any 3' poly-A tail (or, optionally, 5' poly-T tail)…

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illumiprocessor
Desktop

illumiprocessor

A tool to batch process illumina sequencing reads using the excellent…

A tool to batch process illumina sequencing reads using the excellent trimmomatic package. illumiprocessor takes a configuration file that is formatted in Microsoft Windows INI file format. It will…

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BCL2FASTQ…
Desktop

BCL2FASTQ Conversion Software

A tool to handle bcl conversion and demultiplexing. Version 1.8.4 has added…

A tool to handle bcl conversion and demultiplexing. Version 1.8.4 has added ability to mask multiple adapter sequences per read, has standard Illumina adapter sequences included in the bcl2fastq…

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Reaper
Desktop

Reaper

A program for demultiplexing, trimming and filtering short read sequencing…

A program for demultiplexing, trimming and filtering short read sequencing data. Reaper is intended to be suitable for dealing with a wide range of sequencing protocols, and will be updated to…

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sabre
Desktop

sabre

A barcode demultiplexing and trimming tool for FastQ files. sabre will…

A barcode demultiplexing and trimming tool for FastQ files. sabre will demultiplex barcoded reads into separate files. It will work on both single-end and paired-end data in fastq format. It simply…

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Scythe
Desktop

Scythe

Uses a Naive Bayesian approach to classify contaminant substrings in sequence…

Uses a Naive Bayesian approach to classify contaminant substrings in sequence reads.

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SeqPrep
Desktop

SeqPrep

A program to merge paired end Illumina reads that are overlapping into a single…

A program to merge paired end Illumina reads that are overlapping into a single longer read.

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Sickle
Desktop

Sickle

A windowed adaptive trimming tool for FASTQ files using quality.

A windowed adaptive trimming tool for FASTQ files using quality.

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GBS barcode…
Desktop

GBS barcode splitter

The PERL script is used to split barcode of Illumina sequencing data created by…

The PERL script is used to split barcode of Illumina sequencing data created by GBS protocol (www.maizegenetics.net).

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ea-utils
Desktop

ea-utils

A command-line tools for processing biological sequencing data. Barcode…

A 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…

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FASTX-Toolkit
Desktop

FASTX-Toolkit

A collection of command line tools for Short-Reads FASTA/FASTQ files…

A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple short-reads sequences…

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