612 Open source projects that are alternatives of or similar to streamformatics

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

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

Graph Explorer

Syntax highlighting for computational biology

Toolkit for preparing genomes for submission to NCBI

The sources of the openSNP website

A computational library for learning and evaluating biological knowledge graph embeddings

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

Computational Analysis of Novel Drug Opportunities

Next generation sequencing reads de novo assembler.

Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests

R package for analyzing single-cell RNA-seq data

The Ensembl Compara Perl API and SQL schema

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

A treemap interactive chart web component for visualizing hierarchical data

parallel fastq-dump wrapper

A simple command-line tool to download data from Joint Genome Institute databases

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

😠 UpSet.js - a set visualization library for rendering UpSet Plots (a JavaScript re-implementation of UpSet(R) by Lex et al), Euler Diagrams, Venn Diagrams, and Karnaugh Maps

A partition / icicle interactive chart web component for visualizing hierarchical data

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

A modular annotation tool for genomic 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:

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

nim wrapper for htslib for parsing genomics data files

Tutorial on real-time data visualization. Python websocket server & d3.js + crossfilter.js frontend

Welcome to the website and github repository for the Genome Analysis Module. This website will guide the learning experience for trainees in the UBC MSc Genetic Counselling Training Program, as they embark on a journey to learn about analyzing genomes.

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

InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

Provide R access to the NCI Genomic Data Commons portal.

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

Visual tool to spot odd runtime behaviour of Haskell programs.

Single cell perturbation prediction

Examples using Clustergrammer2 to explore high-dimensional datasets.

Application for making ENCODE Blacklists

A snake game trained using simple deep learning implemented in client side javascript.

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

Useful bioinformatic scripts

APBS - software for biomolecular electrostatics and solvation

Long read / genome alignment software

An efficient FASTQ manipulation suite

WebLogo 3: Sequence Logos redrawn

UGENE is free open-source cross-platform bioinformatics software

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

Benchmarking programming languages/implementations for common tasks in Bioinformatics

My own tools code for NGS data analysis (Next Generation Sequencing)

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

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

A Practical and Efficient NCBI Taxonomy Toolkit

VirNet: A deep attention model for viral reads identification

Code examples for the book Mastering D3.js, published in August 2014 by Packt Publishing.

Vue sunburst component based on D3.js

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

This library tackles the construction and efficient execution of computational chemistry workflows

The uncompromising Snakemake code formatter

DOM Text Based Multiple Sequence Alignment Library

𝙋𝙝𝙮𝙡𝙤𝙜𝙚𝙣𝙚𝙩𝙞𝙘 𝘾𝙤𝙢𝙥𝙤𝙣𝙚𝙣𝙩 𝙂𝙧𝙖𝙥𝙝 ⸺ Haskell program and libraries for general phylogenetic graph search

Fast motif matching in R

Simple pure Python SAM parser and objects for working with SAM records