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

Tools for working with SAM/BAM data

Classify sequencing reads using MinHash.

Race and ethnicity Imputation from Disease history with Deep LEarning

Single Cell Analysis Pipelines

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

A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.

A library for generating an interactive SVG visualization of CWL workflows

Protwis is the backbone of the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).

A fast and sensitive gapped read aligner

A permissively licensed library designed to replace Illumina's Experiment Manager

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

Genomics using open source tools, running on GCP or AWS

Plant image analysis using OpenCV

R mased batch sequence downloader, with primer development and in silico evaluation capabilities

Support Vector Structural Variation Genotyper

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

Ultra-fast and memory-efficient (meta-)genome assembler

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

Genomics Extension for SQLite

A faster lmm for GWAS. Supports GPU backend.

A scikit-learn compatible library for graph kernels

Structural variation caller using third generation sequencing

Yet Another Chimeric Read Detector

Dash for Julia - A Julia interface to the Dash ecosystem for creating analytic web applications in Julia. No JavaScript required.

Open-source bioinformatics components for Dash

JavaScript VisualizationTools

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

Core BioPerl 1.x code

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

Strelka2 germline and somatic small variant caller

Analysis pipelines for sequencing data

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

Efficient pythonic random access to fasta subsequences

Examples of using deep learning in Bioinformatics

MOLGENIS - for scientific data: management, exploration, integration and analysis.

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

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

🔬 Assemble large genomes using short reads

VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.

React component for Cytoscape.js network visualisations

Therapeutics Data Commons: Machine Learning Datasets and Tasks for Therapeutics

A curated list of resources for learning bioinformatics.

A tool to circularize genome assemblies

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

Accurate sample inference from amplicon data with single nucleotide resolution

Intuitive local web frontend for the BLAST bioinformatics tool

Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).

Python package for graph neural networks in chemistry and biology

An analysis and visualization platform for 'omics data

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

A curated list of awesome Bioinformatics libraries and software.

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

Simple simulation of single-cell RNA sequencing data

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

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

APBS - software for biomolecular electrostatics and solvation

Inference of ploidy and heterozygosity structure using whole genome sequencing data

The START App: R Shiny Transcriptome Analysis Resource Tool

A robust model for quantitative comparison of ChIP-Seq data sets.

A computational library for learning and evaluating biological knowledge graph embeddings