Stars
Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
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.
ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the scenario where high quality proteins from one or several close…
整理常用的群体遗传学分析流程和脚本
Practical, reusable scripts for bioinformatics
Tools for working with second gen assemblies, fasta sequences, etc
A Circos-based tool to visualize genome assembly consistency or synteny between assemblies.
ViewBS - a powerful toolkit for visualization of high-throughput bisulfite sequencing data
Few scripts facilitating the extraction of info from Repeat Masker .out files
Concatenates FASTA formatted files to one "phyml" (PHYLIP) formatted file
Bioinformatics scripts produced over the course of my work. Now maintained on GitLab.
Genome Scripts used in fungal comparative genomics
Tool set for processing fasta/fastq/table formated data. Usually they are perl scripts.
BITACORA: A Bioinformatics tool for gene family annotation
Multi-level visualization of genomic statistical variables on rectangular chromosomes
use long sequenced reads to close gaps in assemblies
Source code from Zhang et al., (2014) Genomic data of avian phylogenomics project. GigaScience 3:26