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gramtools

Genome inference from a population reference graph

graphaligner

Seed-and-extend program for aligning long error-prone reads to genome graphs.

graphchainer

An accurate aligner of long reads to a variation graph, based on co-linear chaining

graphlan

High-quality circular representations of taxonomic and phylogenetic trees

graphmap2

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1

graphtyper

Population-scale genotyping using pangenome graphs

gridss

GRIDSS: the Genomic Rearrangement IDentification Software Suite

grocsvs

Genome-wide reconstruction of complex structural variants

groopm

Metagenomic binning suite

gsalign

GSAlign: an ultra-fast sequence alignment algorithm for intra-species genome comparison

gsmer

Strain/species identification in metagenomes using genome-specific markers

gsva

Gene set variation analysis

gtctovcf

Script to convert GTC/BPM files to VCF

gtdbtk

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

gtotree

A user-friendly workflow for phylogenomics

gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

guideline-for-computational-biology-and-bioinformatics

hackbrowserdata

Decrypt passwords/cookies/history/bookmarks from the browser. 一款可全平台运行的浏览器数据导出解密工具。

hail

Scalable genomic data analysis.

hal

Hierarchical Alignment Format

halign

a multiple sequence alignment tool

hapcut

program for haplotype phasing from sequence reads and related tools

hapcut2

software tools for haplotype assembly from sequence data

haplosim

Simulate haplotypes according to a random markovian chain along a binary evolutionnary tree and generate metagenomic illumina data from a random admixture of simulated haplotypes

heu_kms_activator

hh-suite

Remote protein homology detection suite.

hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

hinge

Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution"

hisat2

Graph-based alignment (Hierarchical Graph FM index)

hmmer

HMMER: biological sequence analysis using profile HMMs