Get up and running with Llama 3.3, Mistral, Gemma 2, and other large language models.

Run your own AI cluster at home with everyday devices 📱💻 🖥️⌚

This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.

non-redundant, compressed, journalled, file-based storage for biological sequences

HGVS variant name parsing and generation

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

A simple Python implementation of R-PCA

The nimble & robust variant annotator

TransVar - multiway annotator for precision medicine

Plugins for the Ensembl Variant Effect Predictor (VEP)

🦀 Fqkit: A simple and cross-platform program for fastq file manipulation

Declarative visualization library for Python

tools for working with genome variation graphs

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

[HELP REQUESTED] Generalized Additive Models in Python

Benchmarking programming languages/implementations for common tasks in Bioinformatics

A versatile pairwise aligner for genomic and spliced nucleotide sequences

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtool…

Performant Pythonic GenomicRanges

Allocates text labels in matplotlib

A small library for automatically adjustment of text position in matplotlib plots to minimize overlaps.

Create web-based user interfaces with Python. The nice way.

Nextflow DSL2 implementations of pipeline modules for bacterial (nanopore) genomics 🦎

Template for creating Nextflow DSL2 pipelines

A simple DSL2 workflow: tutorial

Nextflow training material for introductory tutorial