Python programs for processing GFF3 files

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.

Toolkit for processing sequences in FASTA/Q formats

NOVOPlasty - The organelle assembler and heteroplasmy caller

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

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Python package and CLI for whole-genome duplication related analyses

A comprehensive tutorial about GWAS and PRS

Coding Genome Reconstruction using Iso-Seq data

A single molecule sequence assembler for genomes large and small.

Accurate Species TRee ALgorithm

Normalizing Hi-C contact counts efficiently

Phylogenetic orthology inference for comparative genomics

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

A full-featured download manager.

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

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

ATAC-seq processing pipeline

3D de novo assembly (3D DNA) pipeline

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

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

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

Evaluation scripts for IsoCon + targeted sequencing approach

Docker for Juicer

autommated annotation pipeline for whole-transcriptome assemblies