biodiversity genomics course by Nicol Rueda, Karin Näsvall and Joana Meier from the Wellcome Sanger Institute

Tutorials on phylogenetic and phylogenomic inference

This pipeline analyses data for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.

Functional modules for analysing single cell omics data.

Single Nucleus Analysis Pipeline for ATAC-seq

De novo assembly from Oxford Nanopore reads.

Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)

ArchaicSeeker is a series of software for detecting archaic introgression sequences and reconstructing introgression history. The latest version of this series, ArchaicSeeker 2.0, has the following…

The genomic data for Papaver species

python module to plot beautiful and highly customizable genome browser tracks

SINE annotation tool for plant genomes

Accurate Species TRee ALgorithm IV (Warning: a bleeding edge version)

learning basics

Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.

Best practices and workflow for genome annotation

Create genomic databases with SIFT predictions. Input is an organism's genomic DNA (.fa) file and the gene annotation file (.gtf). Output will be a database that can be used with SIFT4G_Annotator.j…

Scripts and other material for the assembly and analysis of ratite genomes.

Comparative genomics of obligate brood parasite and closely related species in Anatidae

This is a phylogeny workflow for batch submission to HPC cluster built with Slurm queue manager

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

PhyloAcc a software to detect the changes of conservation of a genomic region

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

Convert genomic coordinates of contact pairs from one assembly to another.

Fast alignment and preprocessing of chromatin profiles

Whole genome alignments using LastZ software in vertebrate species. Code (1) drives embarrassingly parallel execution of commands, (2) merge output into sensible formats and (3) provides ways to dr…

TSEBRA: Transcript Selector for BRAKER

Mikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data * and to select the best models in each locus.

Genome annotation with AUGUSTUS