[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome

Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy

MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (only v4) to detect Structural Variation

Workflow for Building Microsynteny Networks

Components of genome sequence assembly tools

Small and simple scripts useful for various bioinformatics purposes e.g. extract sequences from fasta files

A ToolKit to perform a Meta-analysis of Genome-Wide Association Studies

DEPRECATED: Use Cenote-Taker 3 instead

SARS-CoV-2 Genome Assembler

🐳 Apollo 2.X Docker Image

Detecting transposable element invasions without repeat library. Detects also horizontal transfer events and endogenized viruses. All you need is a reference genome and some short reads

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

⚪ ➡️ 🔍 ℹ️ A suggested workflow, and accompanying scripts, to assemble Single Amplified Genomes (SAGs) from MDA derived Hi/MiSeq (Overlapped) Paired-End Illumina Libraries.

Methods for genome paper

Teaching Material for Course "Computational Bioscience & Machine Learning 2021 - Genome Assembly"

Scripts to index and align Bovine genome with HISAT2

Aphrocallistes vastus genome

Genomics Part of the KAUST High Throughput Sequencing Workshop 2019

🏠 $HOME sweet $HOME

Code of the article that describes the molecular epidemiology analyses of OsHV-1 virus by whole genome sequencing approaches in French shellfish growing areas.