A new bootable USB solution.

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Library for the analysis of networks

MMseqs2: ultra fast and sensitive search and clustering suite

Tools (written in C using htslib) for manipulating next-generation sequencing data

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

De novo assembler for single molecule sequencing reads using repeat graphs

Near-optimal RNA-Seq quantification

Official home of genome aligner based upon notion of Cactus graphs

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

Sequence-to-graph mapper and graph generator

Fast and accurate de novo assembler for long reads

🔬 BEDOPS: high-performance genomic feature operations

Long read / genome alignment software

Fast and accurately polish the genome generated by long reads.

Program for aligning DNA sequences, a pairwise aligner.

software tools for haplotype assembly from sequence data

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

Ultra-fast de novo assembler using long noisy reads

[IMPORTANT: not for real data analysis, only for algorithm evaluation] fast and accurate alignment tool for PacBio and Nanopore long reads

The MARVEL assembler

FALCON-Phase integrates PacBio long-read assemblies with Phase Genomics Hi-C data to create phased, diploid, chromosome-scale scaffolds

Evaluate variant calls and its combination with k-mer multiplicity

A statistical framework for ploidy estimation using NGS short-read data

Pauvre: QC and genome browser plotting Oxford Nanopore and PacBio long reads.

This is *NOT* the official repository of samtools.

A dotplot generator for large chromosomes

Assembly Likelihood Estimator

program for haplotype phasing from sequence reads and related tools