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

Prodigal Gene Prediction Software

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

HMMER: biological sequence analysis using profile HMMs

Align proteins to genomes with splicing and frameshift

Fast and accurate de novo assembler for long reads

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

Program for aligning DNA sequences, a pairwise aligner.

Fast and accurately polish the genome generated by long reads.

Detecting sites of genomic enrichment

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

UCSC command line bioinformatic utilities

Yet another k-mer analyzer

Nanopore data assembler

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.

PHAST

The MARVEL assembler