570 Open source projects that are alternatives of or similar to jgi-query

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

A tool to circularize genome assemblies

NGLess: NGS with less work

A versatile pairwise aligner for genomic and spliced nucleotide sequences

GenomeTools genome analysis system.

Model and predict short DNA sequence features with neural networks

Antimicrobial Resistance Identification By Assembly

Inference of ploidy and heterozygosity structure using whole genome sequencing data

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

Deep learning infrastructure for bioinformatics

cython + htslib == fast VCF and BCF processing

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

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

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

Genomics Extension for SQLite

Bioinformatics library for .NET

A cool place to store your Hi-C

An interactive web tool for quality control of DNA sequencing data

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

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

Ten Quick Tips for Deep Learning in Biology

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

🔬 BEDOPS: high-performance genomic feature operations

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

Data intensive science for everyone.

JavaScript VisualizationTools

Scalable genomic data analysis.

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

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

Analysis pipelines for sequencing data

Official code repository for GATK versions 4 and up

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

Scripts to download genomes from the NCBI FTP servers

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

Bayesian genotyper for structural variants

GCP Essentials for Bioinformatics Researchers

A fast whole-genome aligner based on de Bruijn graphs

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

A collection of scripts and notes related to genomics and bioinformatics

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

Tools to process and analyze deep sequencing data.

Bayesian haplotype-based mutation calling

nim wrapper for htslib for parsing genomics data files

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

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

Reads simulator

Rapid large-scale prokaryote pan genome analysis

A genome browser that shows long reads and complex variants better

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

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

Intuitive local web frontend for the BLAST bioinformatics tool

An ultrafast memory-efficient short read aligner

A powerful open source data warehouse system

The next version of bwa-mem

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

Code examples of fast and simple k-mer counters for tutorial purposes

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

Official git repository for Biopython (originally converted from CVS)

Haplotype VCF comparison tools