398 Open source projects that are alternatives of or similar to Sourmash

Python package for graph neural networks in chemistry and biology

Single cell perturbation prediction

Annotated data.

Application for making ENCODE Blacklists

React component for Cytoscape.js network visualisations

dna2vec: Consistent vector representations of variable-length k-mers

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

APBS - software for biomolecular electrostatics and solvation

RAxML Next Generation: faster, easier-to-use and more flexible

An efficient FASTQ manipulation suite

Syntax highlighting for computational biology

UGENE is free open-source cross-platform bioinformatics software

Analytical Web Apps for Python, R, Julia, and Jupyter. No JavaScript Required.

Benchmarking programming languages/implementations for common tasks in Bioinformatics

The sources of the openSNP website

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

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

A Practical and Efficient NCBI Taxonomy Toolkit

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

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.

A curated list of resources for learning bioinformatics.

A collection of scripts and notes related to genomics and bioinformatics

Next generation sequencing reads de novo assembler.

Inference of ploidy and heterozygosity structure using whole genome sequencing data

A genome browser that shows long reads and complex variants better

Antimicrobial Resistance Identification By Assembly

R package for analyzing single-cell RNA-seq data

A DSL for data-driven computational pipelines

Examples of using deep learning in Bioinformatics

FastQC port to Qt5: A quality control tool for high throughput sequence data.

Package for fetching metadata and downloading data from SRA/ENA/GEO

Bioinformatics library for .NET

Deep learning infrastructure for bioinformatics

A robust and fast clustering method for amplicon-based studies

parallel fastq-dump wrapper

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

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

A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.

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

Metadata and website for the Open Bio Ontologies Foundry Ontology Registry

Toolset for SV simulation, comparison and filtering

Structural variant toolkit for VCFs

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

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

🔬 Assemble large genomes using short reads

EDAM is an ontology of bioinformatics types of data including identifiers, data formats, operations and topics.

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:

Bayesian genotyper for structural variants

Reads simulator

Biological sequences for the julia language

nim wrapper for htslib for parsing genomics data files

An interactive web tool for quality control of DNA sequencing data

Intuitive local web frontend for the BLAST bioinformatics tool

Simple simulation of single-cell RNA sequencing data

🍺🔬 Bioinformatics formulae for the Homebrew package manager (macOS and Linux)

Remote protein homology detection suite.

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

A powerful open source data warehouse system

Cuneiform distributed programming language

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Salentin et al. (2015), https://www.doi.org/10.1093/nar/gkv315