499 Open source projects that are alternatives of or similar to Khmer

Data intensive science for everyone.

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

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

Fast hash function for DNA sequences

A collection of scripts and notes related to genomics and bioinformatics

Analysis pipelines for sequencing data

A curated list of awesome bioinformatics software.

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

Official git repository for Biopython (originally converted from CVS)

Official code repository for GATK versions 4 and up

Efficient pythonic random access to fasta subsequences

A package for designing compact and comprehensive capture probe sets.

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

🔬 Assemble large genomes using short reads

UGENE is free open-source cross-platform bioinformatics software

Fast and flexible ORF finder

A fast 23andMe genome text file parser, now superseded by arv

Open-source bioinformatics components for Dash

Bioinformatics containers

Java utilities for Bioinformatics

Bioinformatics one liners from Ming Tang

BWK awk modified for biological data

The FASTEST QUALITY hash function, random number generators (PRNG) and hash map.

A comprehensive tutorial about GWAS and PRS

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

The next version of bwa-mem

Therapeutics Data Commons: Machine Learning Datasets and Tasks for Therapeutics

Working with molecular structures in pandas DataFrames

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

16,432 Free Yara rules created by

Biostar Q&A

Interactive network visualization in Python and Dash, powered by Cytoscape.js

A cross-platform command-line tool for executing jobs in parallel

List of Computer Science courses with video lectures.

🎯 Bloom filters for C++11

Tools for working with SAM/BAM data

Modular and universal bioinformatics

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

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

The Chemistry Development Kit

Accurate sample inference from amplicon data with single nucleotide resolution

An open source platform for managing and analyzing biomedical big data

Unix, R and python tools for genomics and data science

C library for high-throughput sequencing data formats

Tools to process and analyze deep sequencing data.

A modern genome browser built with JavaScript and HTML5.

An analysis and visualization platform for 'omics data

Structural variant and indel caller for mapped sequencing data

A fast and sensitive gapped read aligner

Fast, reliable cuckoo hash table for Node.js.

COBRApy is a package for constraint-based modeling of metabolic networks.

Versatile open-source tool for microbiome analysis

Signal-level algorithms for MinION data

LUA Redis scripts for a scaling bloom filter

A high-performance, Pythonic language for bioinformatics

Plant image analysis using OpenCV

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

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

Scripts to download genomes from the NCBI FTP servers

MMseqs2: ultra fast and sensitive search and clustering suite