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gatk

Official code repository for GATK versions 4 and up

gemma

Genome-wide Efficient Mixed Model Association

genomics_general

General tools for genomic analyses.

ggcor

Extended tools for correlation analysis and visualization.

ggseqlogo

Publication-quality sequence logos in R

gtz

A high performance and compression ratio compressor, powered by GTXLab of Genetalks.

handycnv

An R package for Standardized Summary, Annotation, Comparison, and Visualization of CNV, CNVR and ROH

hera

hmmratac

HMMRATAC peak caller for ATAC-seq data

hosts

镜像：https://coding.net/u/scaffrey/p/hosts/git

hupan

Human pan-genome analysis pipeline

idr

IDR

indel_correction_pipeline

new falcon assemblies that have been quivered and Pilon polished still have heterozygote indel errors. This pipeline will correct most of them.

jbrowse

A modern genome browser built with JavaScript and HTML5.

jelly2

A gap filling tool for genomes that utilizes PacBio long reads

ldhat

Estimate recombination rates from population genetic data

leaflet

R Interface to Leaflet Maps

leafletcn

An R gallery for China and other geojson choropleth map in leaflet

logomaker

Software for the visualization of sequence-function relationships

lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery

maize_v4_te_annotation

scripts and intermediate files used to annotate TEs in Jiao et al.

mcclintock

Meta-pipeline to identify transposable element insertions using next generation sequencing data

menthu

Repository for MENTHU knockout site recommender

mo17_genome_assembly

mutmap

MutMap pipeline to identify causative mutations responsible for a phenotype

mygene.py

mygene is an easy-to-use Python wrapper to access MyGene.Info services.

nextpolish

Fast and accurately polish the genome generated by noisy long reads.

ngs-pipeline

By study this, it won't be costly or time-consuming to customize a NGS data analysis pipeline

organelle_pba

A software to assemble chloroplast and mitochodrial genomes using PacBio data

owltools

OWLTools