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fermikit

De novo assembly based variant calling pipeline for Illumina short reads

foreign

Modified or extracted from other programs

gdown.pl

Google Drive direct download of big files

gfa-spec

Graphical Fragment Assembly (GFA) Format Specification

gfa1

This repo is deprecated. Please use gfatools instead.

gfatools

Tools for manipulating sequence graphs in the GFA and rGFA formats

gffio

ggml

Tensor library for machine learning

gnuplot-colorbrewer

ColorBrewer color schemes for gnuplot

gwfa

Proof-of-concept implementation of GWFA for sequence-to-graph alignment

hapdip

The CHM1-NA12878 benchmark for single-sample SNP/INDEL calling from WGS Illumina data

hickit

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

hifiasm-meta

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

hpp_year1_assemblies

Assemblies from HPP Year 1 production

hts-specs

Specifications of SAM/BAM and related high-throughput sequencing file formats

htsbox

My experimental tools on top of htslib. NOT OFFICIAL!!!

ibsget

Download files from Illumina BaseSpace (*OUTDATED* as BaseSpace has changed APIs)

jellyfish

A fast multi-threaded k-mer counter

jstreeview

Interactive phylogenetic tree viewer/editor

jtg

JavaScript Turtle Graphics

klib.nim

Experimental getopt, gzip reader, FASTA/Q parser and interval queries in nim-lang

kmer-cnt

Code examples of fast and simple k-mer counters for tutorial purposes

ksw2

Global alignment and alignment extension

lh3-snippets

lh3.github.com

lianti

Tools to process LIANTI sequence data

libdivsufsort

Automatically exported from code.google.com/p/libdivsufsort

lv89

C implementation of the Landau-Vishkin algorithm

mag2gfa

DEPRECATED. Code has been moved to lh3/gfa1/misc

markdown-editor

Live (Github-flavored) Markdown Editor