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minigraph

Sequence-to-graph mapper and graph generator

minimap

This repo is DEPRECATED. Please use minimap2, the successor of minimap.

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

miniprot

Align proteins to genomes with splicing and frameshift

miniwfa

A reimplementation of the WaveFront Alignment algorithm at low memory

misc

Useful small programs

naivepca

Naive PCA for genotype data

nasw

Dynamic programming for aa-to-nt alignment with affine gap, splicing and frameshift

null-buildpack

a heroku buildpack that runs executables

partig

An experimental tool to estimate the similarity between all pairs of contigs

pbsim-pacbio-simulator

This is an updated mirror of the original PacBio Read Simulator

portablecrystal

Portable Crystal binary distributions for Linux on x86_64

pre-pe

Preprocessing paired-end reads produced with experiment-specific protocols

processing-js

A port of the Processing visualization language to JavaScript.

proot-wrapper

Demonstrating the PRoot program

psmc

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

psnw

prototype

publrasm

quartz

A fork of Quartz (QUAlity score Reduction at Terabyte scale)

readfq

Fast multi-line FASTA/Q reader in several programming languages

rmaxcut

An experimental tool to find approximate max-cuts in a large graph

ropebwt

ropebwt2

Incremental construction of FM-index for DNA sequences

rsamtools

Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

rtgeval

Wrapper for RTG's vcfeval; DEPRECATED!

samblaster

samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.

samtools

This is *NOT* the official repository of samtools.

samtools-legacy

For testing only. DON'T USE!

schemas

The upstream repo has been deprecated, so is this one.

sdg

EXPERIMENTAL implementation of side graph