The Top 200 Sequencing Open Source Projects on Github

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The Top 200 Sequencing Open Source Projects on Github

Categories > Science > Sequencing

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

Deepvariant ⭐ 2,339

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

Official code repository for GATK versions 4 and up

Fastp ⭐ 1,088

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

Data intensive science for everyone.

Simple & Efficient data access for Scala and Scala.js

Mosdepth ⭐ 415

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

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

De novo assembly from Oxford Nanopore reads.

Sequenceserver ⭐ 217

Intuitive local web frontend for the BLAST bioinformatics tool

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.

Rapid large-scale prokaryote pan genome analysis

Afterqc ⭐ 157

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

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

Snapatac ⭐ 140

Analysis Pipeline for Single Cell ATAC-seq

Rnaseq Workflow ⭐ 133

A repository for setting up a RNAseq workflow

Artemis ⭐ 127

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

Circlator ⭐ 127

A tool to circularize genome assemblies

UGENE is free open-source cross-platform bioinformatics software

Genomics ⭐ 117

A collection of scripts and notes related to genomics and bioinformatics

Truvari ⭐ 111

Structural variant toolkit for VCFs

Mercury ⭐ 111

A minimal and human-readable language and environment for the live coding of algorithmic electronic music.

Genomicsqlite ⭐ 104

Genomics Extension for SQLite

Antimicrobial Resistance Identification By Assembly

Snp Sites ⭐ 101

Finds SNP sites from a multi-FASTA alignment file

Nextclade ⭐ 94

Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

Accurate and flexible loops calling tool for 3D genomic data.

BAM Statistics, Feature Counting and Annotation

Polyrhythmic Sequencer library for Web Audio API.

Insilicoseq ⭐ 78

🚀 A sequencing simulator

Fastq.bio ⭐ 75

An interactive web tool for quality control of DNA sequencing data

Generate consensus reads to reduce sequencing noises and remove duplications

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

Xr Abstractions ⭐ 68

a set of abstractions written for pure data, including sequencers, guis, and other utilities.

Mirdeep2 ⭐ 68

Discovering known and novel miRNAs from small RNA sequencing data

Deepnovo ⭐ 67

Protein Identification with Deep Learning

Assembly Stats ⭐ 62

Get assembly statistics from FASTA and FASTQ files

V-pipe is a pipeline designed for analysing NGS data of short viral genomes

Idseq Web ⭐ 58

Infectious Disease Sequencing Platform

xHLA: Fast and accurate HLA typing from short read sequence data

An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19.

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

Analysis pipelines for sequencing data

Hmmratac ⭐ 49

HMMRATAC peak caller for ATAC-seq data

FASTQ compression

A package for designing compact and comprehensive capture probe sets.

Fluentdna ⭐ 43

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.

Assembly_improvement ⭐ 39

Improve the quality of a denovo assembly by scaffolding and gap filling

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

Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files

Pathogen Informatics Training ⭐ 38

Galaxy Rna Workbench ⭐ 38

Galaxy RNA workbench

de novo virus assembler of Illumina paired reads

Tools for analyzing 10X Genomics data

Wisecondorx ⭐ 35

WisecondorX — An evolved WISECONDOR

Maximum likelihood demultiplexing

AStarix: Fast and Optimal Sequence-to-Graph Alignment

A RepSeq processing swiss-knife

Seqcluster ⭐ 32

small RNA analysis from NGS data

Cloud-based single-cell copy-number variation analysis tool

Python3 scripts to manipulate FASTA and FASTQ files

Differential abundance (DA) analysis for microbial absolute abundance data

Bac Genomics Scripts ⭐ 28

Collection of scripts for bacterial genomics

RNASeq pipeline

Deepstats ⭐ 27

deepStats: a stastitical toolbox for deeptools and genomic signals

parallelized blat with multi-threads support

Framework for Metastatic And Clonal History INtegrative Analysis

Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)

Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer

CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria

Microbiomeutilities ⭐ 21

The is mostly a wrapper tool using phyloseq and microbiome R packages.

Awesome Sequencing Tech Papers ⭐ 21

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

Seqminer ⭐ 21

Query sequence data (VCF/BCF1/BCF2, Tabix, BGEN, PLINK) in R

Indigo: SNV and InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products

Smallrnaseq ⭐ 20

small rna-seq analysis package

Gff3toembl ⭐ 20

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

Ultra-fast Multi-threaded FASTQ Demultiplexing

Fastq_utils ⭐ 19

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

Helmsman ⭐ 19

highly-efficient & lightweight mutation signature matrix aggregation

Graph Sequencer ⭐ 18

Sort items in a graph using a topological sort while resolving cycles with priority groups

Primavera ⭐ 18

🌸 Python library for primer-based verification of DNA assemblies: primer selection, data analyis, etc.

Nanotunes ⭐ 17

A small music format and an accompanying implementation using OscillatorNode

Tools for producing pseudo-cgh of next-generation sequencing data

Plasmidtron ⭐ 16

Assembling the cause of phenotypes and genotypes from NGS data

Gargammel ⭐ 16

gargammel is an ancient DNA simulator

Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes

Metaboverse ⭐ 16

Visualizing and Analyzing Metabolic Networks with Reaction Pattern Recognition

Double Sided Assembly Line Balancing With Genetic Algorithm ⭐ 15

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

Mlst_check ⭐ 14

Multilocus sequence typing by blast using the schemes from PubMLST

Saffrontree ⭐ 14

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

Seave is a web platform that enables genetic variants to be easily filtered and annotated with in silico pathogenicity prediction scores and annotations from popular disease databases. Seave stores genomic variation of all types and sizes, and allows filtering for specific inheritance patterns, quality values, allele frequencies and gene lists. Seave is open source and deployable locally, or on a cloud computing provider, and works readily with gene panel, exome and whole genome data, scaling from single labs to multi-institution scale.

Fast and accurate sequence demultiplexing

Bio Tradis ⭐ 12

A set of tools to analyse the output from TraDIS analyses

Ancom Bc Code Archive ⭐ 12

Data, scripts, and outputs for the Nat. Comm. paper "Analysis of Composition of Microbiomes with Bias Correction"

Ctdnatools ⭐ 12

R package to work with ctDNA sequencing data

Illumina analysis pipeline

less like viewer for fastq files

Function sequencing reloaded

MinION Open Nucleotide Identifier for Continuous Analysis - an open source pathogen identifier for real-time analysis on MinION output

1-100 of 200 projects

Advertising 📦 9

Application Programming Interfaces 📦 120

Applications 📦 181

Artificial Intelligence 📦 72

Blockchain 📦 70

Build Tools 📦 111

Cloud Computing 📦 79

Code Quality 📦 28

Collaboration 📦 30

Command Line Interface 📦 48

Community 📦 81

Companies 📦 60

Compilers 📦 60

Computer Science 📦 74

Configuration Management 📦 39

Content Management 📦 167

Control Flow 📦 197

Data Formats 📦 77

Data Processing 📦 266

Data Storage 📦 132

Economics 📦 60

Frameworks 📦 198

Graphics 📦 103

Hardware 📦 148

Integrated Development Environments 📦 47

Learning Resources 📦 147

Libraries 📦 119

Lists Of Projects 📦 21

Machine Learning 📦 336

Mapping 📦 61

Marketing 📦 15

Mathematics 📦 55

Messaging 📦 97

Networking 📦 304

Operating Systems 📦 84

Operations 📦 120

Package Managers 📦 52

Programming Languages 📦 229

Runtime Environments 📦 96

Science 📦 42

Security 📦 375

Social Media 📦 26

Software Architecture 📦 70

Software Development 📦 68

Software Performance 📦 57

Software Quality 📦 127

Text Editors 📦 45

Text Processing 📦 131

User Interface 📦 310

User Interface Components 📦 465

Version Control 📦 29

Virtualization 📦 68

Web Browsers 📦 38

Web Servers 📦 25

Web User Interface 📦 194

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