BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.

BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specifi

Bowtie is an ultrafast, memory-efficient short read aligner.

Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Cleaning you

This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline i

Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocation

This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. I

This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. I

The Genome Analysis Toolkit (GATK) is a set of bioinformatic tools for analyzing high-throughput sequencing (HTS) and variant call format (VCF) data.

The Genome Analysis Toolkit (GATK) is a set of bioinformatic tools for analyzing high-throughput sequencing (HTS) and variant call format (VCF) data.

The Genome Analysis Toolkit (GATK) is a set of bioinformatic tools for analyzing high-throughput sequencing (HTS) and variant call format (VCF) data.

Identify and quantify DNA damage patterns in ancient DNA.

MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis

Nanopore sequence read simulator based on statistical characterization.

Disambiguating two species in next generation sequencing data from grafted samples. Operates on DNA or RNA-seq alignments to the two species and separ

A set of command line tools for manipulating high-throughput sequencing (HTS) data in formats such as SAM/BAM/CRAM and VCF. Available as a standalone

Add or Replace Read Groups in an input BAM or SAM file.

This package is aimed at predicting and number of distinct reads and how many will be expected from additional sequencing using an initial sequencing

This package is aimed at predicting and number of distinct reads and how many will be expected from additional sequencing using an initial sequencing

Tool to trim primers of multiplex deep sequencing data.

Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickl

A software package with various utilities for processing alignments in the SAM format, including variant calling and alignment viewing.

The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.

The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.

Subread is a general-purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. It uses a new mapping paradigm called

A flexible read trimming tool for Illumina NGS data

A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.

VarScan, an open source tool for variant detection that is compatible with several short read align-ers.