avilella

snakemake

This is the development home of the workflow management system Snakemake. For general information, see

diamond

Accelerated BLAST compatible local sequence aligner.

progen

Official release of the ProGen models

egpu-switcher

🖥🐧 Setup script for eGPUs in Linux (X.Org)

localcolabfold

ColabFold on your local PC

alphafold_non_docker

AlphaFold2 non-docker setup

Roary

Rapid large-scale prokaryote pan genome analysis

parallel-fastq-dump

parallel fastq-dump wrapper

protein-sequence-models

herro

HERRO is a highly-accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1 or R9.4.1 reads (read length of >= 10 kbps is recommended).

alphafold_finetune

Python code for fine-tuning AlphaFold to perform protein-peptide binding predictions

wgbs_tools

tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies

gfaestus

GFA visualizer, GPU-accelerated using Vulkan

migmap

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

bioinfo-tools

Just a collection of (often poor) scripts to do various bits of bioinformatics stuff I find myself needing to do.

phigaro

Phigaro is a scalable command-line tool for predicting phages and prophages

airrflow

B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework

AlphaLink2

AlphaLink2: Integrating crosslinking MS data into Uni-Fold-Multimer

awesome-conformal-prediction

A professionally curated list of awesome Conformal Prediction videos, tutorials, books, papers, PhD and MSc theses, articles and open-source libraries.

immuneSIM

pre-pe

Preprocessing paired-end reads produced with experiment-specific protocols

dlab-public

Code for the paper "DLAB - Deep learning methods for structure-basedvirtual screening of antibodies"

diff-evol-tree-search

We introduce a differentiable approach to phylogenetic tree construction, optimizing tree and ancestral sequences in its original representation itself, thus requiring no prior training data.

bigwig-nim

command-line querying+conversion of bigwigs and a nim wrapper for dpryan's libbigwig

nanoranger

simplified cellranger for long-read data

ngsderive

Forensic analysis tool useful in backwards computing information from next-generation sequencing data.

Alphafold-analysis

scripts to visualise results of alphafold and alphafold multimer runs

attentive-parapred

Code for Attentive cross-modal paratope prediction

pline

JSON-based web interfaces for command-line programs

Immunoglobulin-repertoire-VH-segment-usage-analysis

This pipeline merges, filters, annotates and calculates the VH gene segment usage in Illumina MiSeq generated paired end B cell immunoglobulin heavy chain sequences. It includes removal of PCR repeats using Unique Molecular Identifiers (UMI).