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Adapter removal software tools | Whole-genome sequencing data analysis

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…
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Trimmomatic
Desktop

Trimmomatic

Performs a variety of trimming tasks for Illumina paired-end and single ended…

Performs a variety of trimming tasks for Illumina paired-end and single ended data. Trimmomatic is a flexible, pair-aware preprocessing tool, optimized for Illumina next-generation sequencing (NGS)…

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NGS-QC Generator
Desktop

NGS-QC Generator Next Generation Sequencing Quality Control generator

Evaluates the quality of ChIP-seq or enrichment-related Next Generation…

Evaluates the quality of ChIP-seq or enrichment-related Next Generation Sequencing (NGS) dataset relative to the datasets present in the entire database through our customized Galaxy platform…

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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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CLC Genomics…
Desktop

CLC Genomics Workbench

Allows to analyze, compare, and visualize next generation sequencing (NGS)…

Allows to analyze, compare, and visualize next generation sequencing (NGS) data. CLC Genomics Workbench offers a complete and customizable solution for genomics, transcriptomics, epigenomics, and…

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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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EAGER
Desktop

EAGER

Permits next-generation sequencing (NGS) analysis to reconstruct ancient…

Permits next-generation sequencing (NGS) analysis to reconstruct ancient genomes. EAGER is able to perform several raw read pre-processing steps, including the initial analysis of raw sequencing…

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FreClu
Desktop

FreClu

Focuses on the broad parent–child relationships hidden in a set of short reads…

Focuses on the broad parent–child relationships hidden in a set of short reads generated from identical experiments with the same starting points. FreClu establishes a novel framework for correcting…

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ShortRead
Desktop

ShortRead

A package for input, quality assessment, manipulation and output of…

A package for input, quality assessment, manipulation and output of high-throughput sequencing data. ShortRead extends Bioconductor with tools useful in the initial stages of short-read DNA sequence…

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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.

oneChannelGUI
Desktop

oneChannelGUI

Facilitates analysis of microarrays and miRNA/RNA-seq data on laptops.…

Facilitates analysis of microarrays and miRNA/RNA-seq data on laptops. oneChannelGUI can be used for quality control, normalization, filtering, statistical validation and data mining for single…

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Chipster
Desktop

Chipster

A user-friendly analysis software tool for high-throughput data. Chipster…

A user-friendly analysis software tool for high-throughput data. Chipster contains over 350 analysis tools for next generation sequencing (NGS), microarray, proteomics and sequence data. Users can…

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NGS-Trex
Web

NGS-Trex NGS TRanscriptome profile EXplorer

Allows user to upload raw sequences and obtain an accurate characterization of…

Allows user to upload raw sequences and obtain an accurate characterization of the transcriptome profile. NGS-Trex can assess differential expression at both gene and transcript level. It compares…

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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

Allows barcode and adapter detection. Flexbar calculates full overlap…

Allows barcode and adapter detection. Flexbar calculates full overlap alignments using Single Instruction Multiple Data (SIMD) and multicore parallelism. It allows to filter reads with uncalled…

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SolexaQA
Desktop

SolexaQA

A user-friendly software package designed to generate detailed statistics and…

A user-friendly software package designed to generate detailed statistics and at-a-glance graphics of sequence data quality both quickly and in an automated fashion. SolexaQA contains associated…

TEtools
Desktop

TEtools transposable elements tools

Provides analysis of TE expression. TEtools takes into account the TE sequence…

Provides analysis of TE expression. TEtools takes into account the TE sequence diversity of the genome. It can be applied to unannotated or unassembled genomes and is freely available under the GPL3.…

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TRAPR
Desktop

TRAPR Total RNA-Seq Analysis Package for R

Facilitates the statistical analysis and visualization of RNA-Seq expression…

Facilitates the statistical analysis and visualization of RNA-Seq expression data. TRAPR provides various functions for data management, the filtering of low-quality data, normalization,…

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ST Pipeline
Desktop

ST Pipeline

Permits to process and analyze the raw files generated with the Spatial…

Permits to process and analyze the raw files generated with the Spatial Transcriptomics (ST) method. ST Pipeline enables demultiplexing of spatially-resolved RNA-seq data and robust quality filtering…

SPLICIFY
Desktop

SPLICIFY

Identifies differentially expressed splice variants on RNA and protein level.…

Identifies differentially expressed splice variants on RNA and protein level. SPLICIFY is able to identify condition-specific aberrant splicing events on protein level by performing comparative…

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QuasR
Desktop

QuasR

Provides an integrated analysis of high-throughput sequencing data in R,…

Provides an integrated analysis of high-throughput sequencing data in R, covering all steps from read preprocessing, alignment and quality control to quantification. QuasR supports different…

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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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TRAPLINE
Desktop

TRAPLINE Transparent Reproducible and Automated PipeLINE

Serves for RNAseq data processing, evaluation and prediction. TRAPLINE guides…

Serves for RNAseq data processing, evaluation and prediction. TRAPLINE guides researchers through the NGS data analysis process in a transparent and automated state-of-the-art pipeline. It can detect…

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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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miARma-Seq
Desktop

miARma-Seq

Designed for mRNA, miRNA and circRNA identification and differential expression…

Designed for mRNA, miRNA and circRNA identification and differential expression analysis, applicable to any sequenced organism. miARma-Seq is presented as a stand-alone tool that provides different…

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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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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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Atropos
Desktop

Atropos

Allows trimming of next-generation sequencing (NGS) reads. Atropos is a…

Allows trimming of next-generation sequencing (NGS) reads. Atropos is a read-trimming tool that has features for Methyl-Seq-specific trimming options, automated adapter detection, estimation of…

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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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ReadTools
Desktop

ReadTools

Provides a toolkit for handling sequence data from different platforms. It…

Provides a toolkit for handling sequence data from different platforms. It evolves with new input file specifications such that it will remain a universal standard for lossless pre-processing…

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LSTrAP
Desktop

LSTrAP Large-Scale Transcriptome Analysis Pipeline

Pre-processes RNA-seq data and maps it to the genome. LSTrAP performs quality…

Pre-processes RNA-seq data and maps it to the genome. LSTrAP performs quality control and produces co-expression networks. It provides functional and comparative genomics data to enable a host of…

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infoTrim
Desktop

infoTrim

Provides a DNA read quality trimmer using entropy. infoTrim is derived from the…

Provides a DNA read quality trimmer using entropy. infoTrim is derived from the maximum information approach of the popular trimmer Trimmomatic. It performs on simulated Sherman bisulfite data and…

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NGS-pipe
Desktop

NGS-pipe

Allows to develop tailored workflows for the analysis of whole-exome (WES),…

Allows to develop tailored workflows for the analysis of whole-exome (WES), whole-genome (WGS), and transcriptome (RNA-seq) sequencing data. NGS-pipe is an automated framework for the design of…

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cutPrimers
Desktop

cutPrimers

Allows to trim primer sequences from amplicon based next generation sequencing…

Allows to trim primer sequences from amplicon based next generation sequencing (NGS) reads. cutPrimers simultaneously searches the primer sequences in the pairs of the reads and enables to remove the…

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zUMIs
Desktop

zUMIs

Processes raw reads to count tables for RNA-seq data using Unique Molecular…

Processes raw reads to count tables for RNA-seq data using Unique Molecular Identifiers (UMIs). zUMIs is a pipeline applicable for most experimental designs of RNA-seq data, such as single-nuclei…

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RNA workbench
Server

RNA workbench

Establishes a central, redistributable workbench for scientists and programmers…

Establishes a central, redistributable workbench for scientists and programmers working with RNA-related data. The RNA workbench builds a sustainable community around it. This platform is unique in…

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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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RNA-Rocket
Web

RNA-Rocket

A free service that provides access to RNA-Seq and ChIP-Seq analysis tools for…

A free service that provides access to RNA-Seq and ChIP-Seq analysis tools for studying infectious diseases. The site makes available thousands of pre-indexed genomes, their annotations, and the…

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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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RAP
Web

RAP RNA-seq Analysis Pipeline

Allows users to analyze sequencing data in multiple steps. The RAP purpose is…

Allows users to analyze sequencing data in multiple steps. The RAP purpose is to investigate the complex transcriptional landscape of eukaryotic transcriptomes through a computationally optimized…

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READemption
Desktop

READemption

Permits the computational evaluation of RNA-Seq data. READemption is an…

Permits the computational evaluation of RNA-Seq data. READemption is an automated RNA-Seq processing with the initial purpose to handle differential RNA-Seq (dRNA-Seq) data for the determination of…

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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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SPARTA
Desktop

SPARTA

Extracts raw Illumina reads to differentially expressed genes. SPARTA is a…

Extracts raw Illumina reads to differentially expressed genes. SPARTA is a bacterial RNA-seq analysis tool performing transcriptional profiling experiments using RNA-seq. It enables microbiologists…

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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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seqyclean
Desktop

seqyclean

Pre-processes next-generation sequencing (NGS) data for preparing downstream…

Pre-processes next-generation sequencing (NGS) data for preparing downstream analysis. Seqyclean is a bioinformatic pipeline for NGS cleaning, including adapter, contaminant, poly A/T and quality…

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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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Fastq_clean
Desktop

Fastq_clean

Cleans the DNA-seq and RNA-seq data from the Illumina sequencer. Fastq_clean is…

Cleans the DNA-seq and RNA-seq data from the Illumina sequencer. Fastq_clean is an optimized pipeline designed to remove the low-quality nucleotides and adapters precisely and keep as many of the…

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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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SPeW
Desktop

SPeW SeqPipeWrap

Allows users to build bioinformatics pipelines.

Allows users to build bioinformatics pipelines.

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Adapter…
Desktop

Adapter Trimming for Small RNA Sequencing

Finds adapter sequences at the 3' end of each read. Adapter Trimming for…

Finds adapter sequences at the 3' end of each read. Adapter Trimming for Small RNA Sequencing gives as output a summary report listing the number of reads of each length after adapter trimming.

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PriLive
Desktop

PriLive

Serves for Ilumina short read sequencing data. PriLive allows users to remove…

Serves for Ilumina short read sequencing data. PriLive allows users to remove human reads from Illumina HiSeq data when they are produced. It permits another level for human genomic privacy and can…

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QCumber
Desktop

QCumber

Aims to explore next-generation sequencing (NGS) data. QCumber allows user to…

Aims to explore next-generation sequencing (NGS) data. QCumber allows user to work about quality control, to extract data from sequence analysis viewer, or to classify reads.

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RiboPip
Desktop

RiboPip

Enables users to process Ribosome Profiling (Ribo-seq) and RNA sequencing…

Enables users to process Ribosome Profiling (Ribo-seq) and RNA sequencing (RNA-seq) datasets. RiboPip computes a splice-aware alignment to a reference database along with a read summarization and…

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Dascrubber
Desktop

Dascrubber DAzzler Read SCRUBBing Suite

Provides a pipeline that one can use to scrub reads and if desired to scrub the…

Provides a pipeline that one can use to scrub reads and if desired to scrub the alignment piles. Dascrubber is a complete end-to-end scrubber for removing all artifacts and low quality segments from…

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BBDuk
Desktop

BBDuk

Filters or trims reads for adapters and contaminants using k-mers. BBDuk was…

Filters or trims reads for adapters and contaminants using k-mers. BBDuk was developed to combine most common data-quality-related trimming, filtering, and masking operations into a single…

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Porechop
Desktop

Porechop

Supports demultiplexing of Nanopore reads that were barcoded with the Native…

Supports demultiplexing of Nanopore reads that were barcoded with the Native Barcoding Kit or PCR Barcoding Kit. Porechop is a python software for finding and removing adapters from Oxford Nanopore…

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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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bcbio-nextgen
Desktop

bcbio-nextgen

A python toolkit providing best-practice pipelines for fully automated high…

A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. You write a high level configuration file specifying your inputs and analysis parameters.…

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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

Allows windowed adaptive trimming. Sickle determines when quality is…

Allows windowed adaptive trimming. Sickle determines when quality is sufficiently low to trim the 3'-end of reads and also when the quality is sufficiently high enough to trim the 5'-end of…

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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

Allows users to process biological sequencing data. ea-utils works with…

Allows users to process biological sequencing data. ea-utils works with pipeline based on Illumina and can run with other FASTQs.

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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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FAR
Desktop

FAR Flexible Adapter Remover

Removes adapter sequences from deep sequencing data in FASTA/Q, CSFASTA/Q…

Removes adapter sequences from deep sequencing data in FASTA/Q, CSFASTA/Q format. FAR is also able to demultiplex barcoded runs.

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