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

Tools for working with genomic and high throughput sequencing data.

MiXCR is a universal software for fast and accurate extraction of T- and B- cell receptor repertoires from any type of sequencing data. Free for academic use only.

GenomeTools genome analysis system.

Curated (meta)list of resources for Biology.

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

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

Bioconductor cheat sheet

🔬 BEDOPS: high-performance genomic feature operations

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

Python for Bioinformatics

Cuneiform distributed programming language

A comprehensive library for computational molecular biology

A powerful open source data warehouse system

A repository for setting up a RNAseq workflow

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

Fast Reference-Guided Scaffolding of Genome Assembly Contigs. RagTag, the successor to RaGOO, is now available here: https://github.com/malonge/RagTag

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

BioGrakn Knowledge Graph

Remote protein homology detection suite.

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

Protein Graph Library

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

A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.

Bayesian haplotype-based mutation calling

Ten Quick Tips for Deep Learning in Biology

Rapid large-scale prokaryote pan genome analysis

nim wrapper for htslib for parsing genomics data files

Intuitive local web frontend for the BLAST bioinformatics tool

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

🔬 Assemble large genomes using short reads

Annotated data.

Python package for graph neural networks in chemistry and biology

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

Examples of using deep learning in Bioinformatics

Syntax highlighting for computational biology

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

The sources of the openSNP website

React component for Cytoscape.js network visualisations

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

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

Next generation sequencing reads de novo assembler.

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

R package for analyzing single-cell RNA-seq data

A genome browser that shows long reads and complex variants better

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

A curated list of resources for learning bioinformatics.

parallel fastq-dump wrapper

Deep learning infrastructure for bioinformatics

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

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

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

Toolset for SV simulation, comparison and filtering

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:

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

Reads simulator

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