Bioinformatics

List of Computer Science courses with video lectures.

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

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

A curated list of awesome Bioinformatics libraries and software.

A DSL for data-driven computational pipelines

Conda recipes for the bioconda channel.

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

Official code repository for GATK versions 4 and up

A versatile pairwise aligner for genomic and spliced nucleotide sequences

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

A full spaCy pipeline and models for scientific/biomedical documents.

Toolkit for processing sequences in FASTA/Q formats

Data intensive science for everyone.

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

Pytorch Repo for DeepGCNs (ICCV'2019 Oral, TPAMI'2021), DeeperGCN (arXiv'2020) and GNN1000(ICML'2021): https://www.deepgcns.org

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang

Aggregate results from bioinformatics analyses across many samples into a single report.

A plotly.js React component from Plotly 📈

Scalable genomic data analysis.

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

Unix, R and python tools for genomics and data science

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

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

MMseqs2: ultra fast and sensitive search and clustering suite

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

Scripts to download genomes from the NCBI FTP servers