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

Intuitive local web frontend for the BLAST bioinformatics tool

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

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

Single cell perturbation prediction

🔬 Assemble large genomes using short reads

Application for making ENCODE Blacklists

Annotated data.

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

Python package for graph neural networks in chemistry and biology

APBS - software for biomolecular electrostatics and solvation

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

An efficient FASTQ manipulation suite

Examples of using deep learning in Bioinformatics

UGENE is free open-source cross-platform bioinformatics software

Syntax highlighting for computational biology

Benchmarking programming languages/implementations for common tasks in Bioinformatics

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

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

The sources of the openSNP website

A Practical and Efficient NCBI Taxonomy Toolkit

React component for Cytoscape.js network visualisations

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.

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

A collection of scripts and notes related to genomics and bioinformatics

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

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Next generation sequencing reads de novo assembler.

Antimicrobial Resistance Identification By Assembly

Quickly search, compare, and analyze genomic and metagenomic data sets.

A DSL for data-driven computational pipelines

R package for analyzing single-cell RNA-seq data

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

A genome browser that shows long reads and complex variants better

Bioinformatics library for .NET

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

A robust and fast clustering method for amplicon-based studies

A curated list of resources for learning bioinformatics.

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

parallel fastq-dump wrapper

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

Deep learning infrastructure for bioinformatics

Metadata and website for the Open Bio Ontologies Foundry Ontology Registry

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

Structural variant toolkit for VCFs

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

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

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

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

Toolset for SV simulation, comparison and filtering

Bayesian genotyper for structural variants

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:

Biological sequences for the julia language

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

nim wrapper for htslib for parsing genomics data files

An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

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

An ultrafast memory-efficient short read aligner

code for reading and processing Allen Institute for Brain Science data

Genome assembly evaluation tool