A versatile pairwise aligner for genomic and spliced nucleotide sequences

MMseqs2: ultra fast and sensitive search and clustering suite

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

Toolkit for processing sequences in FASTA/Q formats

De novo assembler for single molecule sequencing reads using repeat graphs

Near-optimal RNA-Seq quantification

BWK awk modified for biological data

Official home of genome aligner based upon notion of Cactus graphs

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

Prodigal Gene Prediction Software

Fast and accurate de novo assembler for long reads

HMMER: biological sequence analysis using profile HMMs

Align proteins to genomes with splicing and frameshift

Long read / genome alignment software

haplotypic duplication identification tool

UCSC Genome Browser source. "beta" is released version / "master" is testing.

Tools for manipulating sequence graphs in the GFA and rGFA formats

Fast and accurately polish the genome generated by long reads.

Program for aligning DNA sequences, a pairwise aligner.

Detecting sites of genomic enrichment

UCSC command line bioinformatic utilities

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

Nanopore data assembler

Yet another k-mer analyzer

Ultra-fast de novo assembler using long noisy reads

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.

The MARVEL assembler

PHAST