851 Open source projects that are alternatives of or similar to ntHash

ntHash implementation in Rust

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

Very fast, high-quality hash function (non-cryptographic, C) + PRNG

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

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

Inference of ploidy and heterozygosity structure using whole genome sequencing data

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

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

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

Simple pure Python SAM parser and objects for working with SAM records

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

An interactive web tool for quality control of DNA sequencing data

A fast whole-genome aligner based on de Bruijn graphs

Antimicrobial Resistance Identification By Assembly

Genomics Extension for SQLite

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

A tool to circularize genome assemblies

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

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

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

A genome browser that shows long reads and complex variants better

Toolkit for preparing genomes for submission to NCBI

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

JavaScript VisualizationTools

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

A faster lmm for GWAS. Supports GPU backend.

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

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

Bayesian genotyper for structural variants

Model and predict short DNA sequence features with neural networks

GCP Essentials for Bioinformatics Researchers

Bioinformatics library for .NET

A collection of scripts and notes related to genomics and bioinformatics

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

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

NGLess: NGS with less work

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

A cool place to store your Hi-C

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`

Analysis pipelines for sequencing data

Deep learning infrastructure for bioinformatics

Ten Quick Tips for Deep Learning in Biology

GenomeTools genome analysis system.

Reads simulator

Intuitive local web frontend for the BLAST bioinformatics tool

A powerful open source data warehouse system

🔬 BEDOPS: high-performance genomic feature operations

Rapid large-scale prokaryote pan genome analysis

Official git repository for Biopython (originally converted from CVS)

cython + htslib == fast VCF and BCF processing

Haplotype VCF comparison tools

An ultrafast memory-efficient short read aligner

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

Official code repository for GATK versions 4 and up

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

🔬 Assemble large genomes using short reads

A simple command-line tool to download data from Joint Genome Institute databases

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources