Working pipeline for nanopore + illumina data

maker3 annotation for swan genomes using the transcriptomic evidence, homology evidence and de novo prediction

Inquiline comparative genomics project

RNA-seq analyses.

I'm sharing my automation of the 3D_DNA and SALSA Hi-C scaffolding pipelines.

Utilities for identifying somatic variants, even in reference-less species

Full automatic pipelines to mine OR, TAAR, V2R and V1R genes from any vertebrate genome

Scripts, notes and documents about the BIND annotation workflow (BIND: ab initio gene predictions by BRAKER combined with gene predictions INferred Directly from alignment of RNA-Seq evidence to th…

CCGP Repository for the genome assembly working group.

GTExExtractor.2 is a script that will download and parse individual-level GTEx data set for all tissues and GTEx sample IDs. It will show the distribution of expression for a single gene in a multi…

Experiments for GeneMark-EP/EP+ and ProtHint projects

Genomics analyses for Nile tilapia and blue tilapia genomes

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

GTExExtractor is a script that will download and parse individual-level GTEx data set for all tissues and GTEx sample IDs, and output gene RPKMs for the provided gene list that correspond to the ti…

Scripts for studying SVs via graphs constructed from whole-genome-alignment

use (homologous) proteins to scaffold genomes

This repository includes the scripts which were used to simulate the matching success of several UCE probe sets among 400 genomes of different descents.

This repo hosts the scripts used for tracing the evolution history of ruminants TFBS evolution using the birth-death probabilistic model developed by Yokoyama and Zhang et al. 2014 PLoS CB

A pipeline to create UCSC chain and net files given the genome sequences from two species

Scripts for genome alignment, SNP calling, and recombination identification.