zhaokai2014 Goto Github PK

3d-dna

3D de novo assembly (3D DNA) pipeline

alitv-perl-interface

allhic

Genome scaffolding based on HiC data in heterozygous and high ploidy genomes

astral

Accurate Species TRee ALgorithm

atacproc

ATAC-seq processing pipeline

blobtools

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets

cafe

Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.

canu

A single molecule sequence assembler for genomes large and small.

cogent

Coding Genome Reconstruction using Iso-Seq data

gff3toolkit

Python programs for processing GFF3 files

gwa_tutorial

A comprehensive tutorial about GWAS and PRS

haplomerger2

hic-pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

iced

Normalizing Hi-C contact counts efficiently

irscope

isocon_eval

Evaluation scripts for IsoCon + targeted sequencing approach

juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

juicer-docker

Docker for Juicer

lachesis

The LACHESIS software, as described in Nature Biotechnology (http://dx.doi.org/10.1038/nbt.2727)

ltr_retriever

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.

motrix

A full-featured download manager.

novoplasty

NOVOPlasty - The organelle assembler and heteroplasmy caller

orthofinder

Phylogenetic orthology inference for comparative genomics

seqtk

Toolkit for processing sequences in FASTA/Q formats

transcriptx

autommated annotation pipeline for whole-transcriptome assemblies

trimal

A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0

wgd

Python package and CLI for whole-genome duplication related analyses