934 Open source projects that are alternatives of or similar to Artemis

Example client programs for Saphetor's VarSome annotation API

annotate a VCF with other VCFs/BEDs/tabixed files

Deep learning infrastructure for bioinformatics

Ten Quick Tips for Deep Learning in Biology

GCP Essentials for Bioinformatics Researchers

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

Proof-of-concept seq-to-graph mapper and graph generator

Bioinformatics library for .NET

A powerful open source data warehouse system

A fast whole-genome aligner based on de Bruijn graphs

Official git repository for Biopython (originally converted from CVS)

A comprehensive tutorial about GWAS and PRS

Efficient pythonic random access to fasta subsequences

A modern genome browser built with JavaScript and HTML5.

A React web application to query and share any PostgreSQL database.

Java utilities for Bioinformatics

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

📖🔬☕️ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

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

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

A faster lmm for GWAS. Supports GPU backend.

dysgu-SV is a collection of tools for calling structural variants using short or long reads

Collection of scripts for bacterial genomics

Structural variant toolkit for VCFs

Fast hash function for DNA sequences

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

An open-access bioinformatics text

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

A Java API for high-throughput sequencing data (HTS) formats.

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

A curated list of awesome bioinformatics software.

Earl Grey: A fully automated TE curation and annotation pipeline

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

De novo assembly based variant calling pipeline for Illumina short reads

highly-efficient & lightweight mutation signature matrix aggregation

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

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

Fast alignment and preprocessing of chromatin profiles

An open source platform for managing and analyzing biomedical big data

A high-performance, Pythonic language for bioinformatics

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

A fast and sensitive gapped read aligner

Ultra-fast and memory-efficient (meta-)genome assembler

The next version of bwa-mem

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

Scalable genomic data analysis.

A versatile pairwise aligner for genomic and spliced nucleotide sequences

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

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

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

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

Scripts to download genomes from the NCBI FTP servers

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

Model and predict short DNA sequence features with neural networks

Tools to process and analyze deep sequencing data.

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"

Demonstrating best practices for bioinformatics command line tools

Scout - Instruction based research debugger (a poor man's debugger)