Top 66 sequencing open source projects

A Java API for high-throughput sequencing data (HTS) formats.

✭ 220

java genomics sequencing ngs vcf sam dna

A Python library for creating and manipulating musical patterns, designed for use in algorithmic composition, generative music and sonification. Can be used to generate MIDI events, MIDI files, OSC messages, or custom events.

✭ 207

python music midi composition sequencing

Otto

Sampler, Sequencer, Multi-engine synth and effects - in a box! [WIP]

✭ 2,390

C++CMake audio raspberry-pi music ui-design audio-processing synthesizer sequencing synth

Sequenceserver

Intuitive local web frontend for the BLAST bioinformatics tool

✭ 198

ruby hacktoberfest visualization bioinformatics genomics sequencing

Deepvariant

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

✭ 2,404

python C++shell Starlark Dockerfile deep-learning machine-learning tensorflow bioinformatics science genomics sequencing ngs dna genome deep-neural-network deepvariant

Shasta

De novo assembly from Oxford Nanopore reads.

✭ 188

assembly sequencing dna

Snapatac

Analysis Pipeline for Single Cell ATAC-seq

✭ 183

r machine-learning-algorithms sequencing

Roary

Rapid large-scale prokaryote pan genome analysis

✭ 176

perl bioinformatics research genomics sequencing

Rnaseq Workflow

A repository for setting up a RNAseq workflow

✭ 170

r workflow bioinformatics pipeline science sequencing

Afterqc

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

✭ 169

python bioinformatics error filtering sequencing ngs

Hgvs

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

✭ 138

python bioinformatics genomics sequencing

Artemis

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

✭ 135

java bioinformatics research genomics sequencing

Circlator

A tool to circularize genome assemblies

✭ 121

python bioinformatics research genomics sequencing

Ugene

UGENE is free open-source cross-platform bioinformatics software

✭ 112

cpp cross-platform workflow bioinformatics qt5 pipeline science sequencing ngs dna

Genomics

A collection of scripts and notes related to genomics and bioinformatics

✭ 101

r workflow bioinformatics science genomics sequencing vcf dna

Ariba

Antimicrobial Resistance Identification By Assembly

✭ 96

python bioinformatics research genomics sequencing

Genomicsqlite

Genomics Extension for SQLite

✭ 90

sqlite bioinformatics genomics sqlite3 sequencing

Beet.js

Polyrhythmic Sequencer library for Web Audio API.

✭ 87

javascript js library audio music webaudio sequencing

Truvari

Structural variant toolkit for VCFs

✭ 85

python bioinformatics benchmarking sequencing vcf

Fastq.bio

An interactive web tool for quality control of DNA sequencing data

✭ 76

webassembly wasm bioinformatics svelte genomics sequencing

Mirdeep2

Discovering known and novel miRNAs from small RNA sequencing data

✭ 70

perl analysis mapping prediction sequencing

Gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

✭ 67

c bioinformatics research genomics sequencing

Sns

Analysis pipelines for sequencing data

✭ 43

shell bioinformatics analysis pipeline genomics sequencing dna

Gatk

Official code repository for GATK versions 4 and up

✭ 1,002

java spark bioinformatics science genomics sequencing ngs dna genome

Migmap

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

✭ 38

groovy bioinformatics sequencing ngs

Fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

✭ 966

bioinformatics filter adapter quality filtering sequencing ngs

Awesome Sequencing Tech Papers

A collection of publications on comparison of high-throughput sequencing technologies.

✭ 21

awesome-list bioinformatics genomics sequencing

Quagmir

A python-based isomiR quantification and analysis pipeline

✭ 9

python pipeline sequencing

Helmsman

highly-efficient & lightweight mutation signature matrix aggregation

✭ 19

python bioinformatics sequencing vcf

Galaxy

Data intensive science for everyone.

✭ 812

python hacktoberfest docker workflow bioinformatics pipeline science genomics workflow-engine sequencing ngs dna

Fetch

Simple & Efficient data access for Scala and Scala.js

✭ 453

scala data concurrency cats parallelism sequencing monads

Mosdepth

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

✭ 376

nim hacktoberfest coverage sequencing depth genome

gff3toembl

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

✭ 27

python shell TeX Dockerfile bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

pheniqs

Fast and accurate sequence demultiplexing

✭ 14

C++python HTML shell c Makefile CSS autocomplete tagging sequencing barcode sam robust tag bam fastq multiplexing cram demultiplexing classifiers

RNASeq

RNASeq pipeline

✭ 30

perl rna-seq pipeline sequencing rna read-counts

gencore

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

✭ 91

C++bioinformatics duplex ngs sequencing consensus duplication deduplication somatic deep-sequencing sequencing-error sequencing-noise duplex-sequencing

fastq utils

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

Double-Sided-Assembly-Line-Balancing-with-Genetic-Algorithm

Double Sided Assembly Line Balancing with Genetic Algorithm (C#)

✭ 19

C#sequencing genetic-algorithms

plasmidtron

Assembling the cause of phenotypes and genotypes from NGS data

✭ 27

python shell Dockerfile bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

pblat

parallelized blat with multi-threads support

✭ 34

c Makefile shell Roff perl C++genome mapping parallel sequencing multithreading alignment

catch

A package for designing compact and comprehensive capture probe sets.

✭ 55

python science bioinformatics genomics genome ngs sequencing metagenomics dna viral covid-19

saffrontree

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

✭ 17

python TeX shell Dockerfile bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

InSilicoSeq

🚀 A sequencing simulator

✭ 116

python Dockerfile bioinformatics simulation sequencing metagenomics illumina-sequencing

FluentDNA

FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.

✭ 52