genomics

Official git repository for Biopython (originally converted from CVS)

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Official code repository for GATK versions 4 and up

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

Data intensive science for everyone.

A collaboratively written review paper on deep learning, genomics, and precision medicine

tools for working with genome variation graphs

🧬 gget enables efficient querying of genomic reference databases

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

Scripts to download genomes from the NCBI FTP servers

Cloud-native genomic dataframes and batch computing

Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)

A comprehensive tutorial about GWAS and PRS

Python library to handle Gene Ontology (GO) terms

Python library to facilitate genome assembly, annotation, and comparative genomics

Python and C++ code for reading and writing genomics data.

The next version of bwa-mem

Tools to process and analyze deep sequencing data.

A fast and sensitive gapped read aligner