1458 Open source projects that are alternatives of or similar to Deep Rules

Scripts to download genomes from the NCBI FTP servers

An open-access bioinformatics text

Java utilities for Bioinformatics

A powerful open source data warehouse system

Efficient variant-call data storage and retrieval library using the TileDB storage library.

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

A modern genome browser built with JavaScript and HTML5.

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

课题组每周研讨会

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

Javascript full-stack framework for Big Data visualisation and analysis

Annotated data.

Single-Cell Analysis in Python. Scales to >1M cells.

Python Programming for Biologists

Parser and database to index the terpene profile of different strains of Cannabis from online databases

Provides access to complex Bioinformatics software (even BioLinux!) in just one command.

A list of web-based interactive biological data visualizations.

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

An interactive web tool for quality control of DNA sequencing data

Biological sequences for the julia language

GCP Essentials for Bioinformatics Researchers

Antimicrobial Resistance Identification By Assembly

A collection of scripts and notes related to genomics and bioinformatics

Data intensive science for everyone.

Scalable genomic data analysis.

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

NGLess: NGS with less work

A versatile pairwise aligner for genomic and spliced nucleotide sequences

A collection of publications on comparison of high-throughput sequencing technologies.

MetaSRA: normalized sample-specific metadata for the Sequence Read Archive

Unix, R and python tools for genomics and data science

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

Analysis pipelines for sequencing data

Model and predict short DNA sequence features with neural networks

Official code repository for GATK versions 4 and up

Flexible genotype query among 30,000+ samples whole-genome

Global Biotic Interactions provides access to existing species interaction datasets

A fast whole-genome aligner based on de Bruijn graphs

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

Rapid large-scale prokaryote pan genome analysis

Race and ethnicity Imputation from Disease history with Deep LEarning

Bioinformatics library for .NET

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Genomics Extension for SQLite

A cool place to store your Hi-C

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

A tool to circularize genome assemblies

List of tools and resources related to the 10x Genomics GEMCode/Chromium system

nim wrapper for htslib for parsing genomics data files

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

Bayesian haplotype-based mutation calling

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Curated (meta)list of resources for Biology.

A curated list of bioinformatics bench-marking papers and resources.