A curated list of awesome Machine Learning frameworks, libraries and software.

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Machine Learning Engineering Open Book

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

Data intensive science for everyone.

Collection of bioinformatics training materials

Scripts to download genomes from the NCBI FTP servers

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

Fast genome-wide functional annotation through orthology assignment

Copy number variant detection from targeted DNA sequencing

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

Tools for fast and flexible genome assembly scaffolding and improvement

Quickly search, compare, and analyze genomic and metagenomic data sets.

An analysis and visualization platform for 'omics data

genes and genomes at your fingertips

ATLAS - Three commands to start analyzing your metagenome data

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.

Read-based phasing of genomic variants, also called haplotype assembly

Structural variant toolkit for VCFs

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

Eukaryotic Genome Annotation Pipeline

Bioinformatics data analysis and visualization toolkit

a lightweight db framework for exploring genetic variation.

Variational autoencoder for metagenomic binning

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

minimal example implementations for bioinformatics workflow managers

customizable pipeline to identify viral sequences from (meta)genomic data

CloudBioLinux: configure virtual (or real) machines with tools for biological analyses

💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data