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flappie

Flip-flop basecaller for Oxford Nanopore reads

flye

De novo assembler for single molecule sequencing reads using repeat graphs

freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

funannotate

Eukaryotic Genome Annotation Pipeline

fungap

FunGAP: fungal Genome Annotation Pipeline

genespace

genodup-pipeline

This python script can be used to detect Whole-genome duplication (WGD) with the dS based method.

genome-annotation

A nextflow pipeline with automatic software provisioning to generate hints and subsequent genome model predictions with AUGUSTUS

genome_coverage_plotter

Simple script to generate whole-genome coverage plots

get_homologues

GET_HOMOLOGUES: a versatile software package for pan-genome analysis

get_phylomarkers

A pipeline to select optimal markers for microbial phylogenomics, population genetics and genomic taxonomy

gganimate

A Grammar of Animated Graphics

ggforce

Accelerating ggplot2

gggenomes

A grammar of graphics for comparative genomics

ggraph

Grammar of Graph Graphics

goatools

Python scripts to find enrichment of GO terms

graphlayouts

new layout algorithms for network visualizations in R

gwa_tutorial

A comprehensive tutorial about GWAS and PRS

hal

Hierarchical Alignment Format

heatmaply

Interactive Heat Maps for R Using plotly

higlass

Fast large scale matrix visualization for the web.

jcvi

Python utility libraries on genome assembly, annotation and comparative genomics

jmodeltest2

Automatically exported from code.google.com/p/jmodeltest2

juicebox

Visualization and analysis software for Hi-C data -

lathe

A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing

liftoff

An accurate GFF3/GTF lift over pipeline

lotus2

Amplicon sequencing pipelines suitable for 16S, 18S and ITS.

make_silva_db

General procedure for making QIIME 2 compatible SILVA reference files

markdown-here

Google Chrome, Firefox, and Thunderbird extension that lets you write email in Markdown and render it before sending.

mcscan

Command-line program to wrap dagchainer and combine pairwise results into multi-alignments in column format