BEDTools is an extensive suite of utilities for comparing genomic features in BED format.

Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.

A tool that finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and c

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

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning read

Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectatio

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

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

User-friendly tools for the normalization and visualization of deep-sequencing data.

User-friendly tools for the normalization and visualization of deep-sequencing data.

User-friendly tools for the normalization and visualization of deep-sequencing data.

DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classif

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

Tool for predicting effects of variants for any genome in Ensembl or with genome annotation (via GFF). This includes vertebrates and also plants, fung

A simple way to screen a library of short reads against a set of reference libraries. Its most common use is as part of a QC pipeline to confirm that

Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events

Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events

High-performance visualization tool for interactive exploration of large, integrated datasets. It supports a wide variety of data types and format, in

Short read alignment program incorporating quality scores

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

Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps

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.

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

Tool for predicting effects of variants for any genome in Ensembl or with genome annotation (via GFF). This includes vertebrates and also plants, fung