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The Top 2,265 Sequencing Open Source Projects

Categories > Science > Sequencing
Deepvariant ⭐ 2,457
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
most recent commit 4 months ago
Ncov ⭐ 1,290
Nextstrain build for novel coronavirus SARS-CoV-2
most recent commit 2 days ago
Gatk ⭐ 1,258
Official code repository for GATK versions 4 and up
dependent packages 2total releases 44most recent commit 5 days ago
Fastp ⭐ 1,248
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging.
most recent commit 2 months ago
Samtools ⭐ 1,215
Tools (written in C using htslib) for manipulating next-generation sequencing data
most recent commit 7 days ago
Galaxy ⭐ 971
Data intensive science for everyone.
dependent packages 12total releases 13most recent commit 2 hours agopypi galaxy-util} Downloads
Adam ⭐ 927
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
dependent packages 17total releases 14most recent commit 25 days ago
Picard ⭐ 779
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
dependent packages 12total releases 171most recent commit 6 days ago
Getting Started With Genomics Tools And Resources ⭐ 754
Unix, R and python tools for genomics and data science
most recent commit a month ago
Htslib ⭐ 625
C library for high-throughput sequencing data formats
dependent packages 1total releases 9most recent commit a day agocargo hts-sys} Downloads
Rna Seq Analysis ⭐ 614
RNAseq analysis notes from Ming Tang
most recent commit 8 months ago
Macs ⭐ 540
MACS -- Model-based Analysis of ChIP-Seq
dependent packages 1total releases 36most recent commit 4 months agopypi MACS2} Downloads
Deeptools ⭐ 502
Tools to process and analyze deep sequencing data.
most recent commit 4 months ago
Uncalled ⭐ 485
Raw nanopore signal mapper that enables real-time targeted sequencing
most recent commit a month ago
Mosdepth ⭐ 478
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
most recent commit 2 months ago
Fetch ⭐ 477
Simple & Efficient data access for Scala and Scala.js
dependent packages 7total releases 23most recent commit 7 days ago
Rnaseq ⭐ 462
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
most recent commit a month ago
Cutadapt ⭐ 404
Cutadapt removes adapter sequences from sequencing reads
most recent commit 5 days ago
Phyloseq ⭐ 396
phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
most recent commit 7 months ago
Scrnaseq Analysis Notes ⭐ 367
scRNAseq analysis notes from Ming Tang
most recent commit a month ago
Hisat2 ⭐ 345
Graph-based alignment (Hierarchical Graph FM index)
most recent commit 4 months ago
Cnvkit ⭐ 337
Copy number variant detection from targeted DNA sequencing
total releases 49most recent commit 3 months ago
Elm D3 ⭐ 328
Elm bindings for D3.js
most recent commit 6 years ago
Sniffles ⭐ 323
Structural variation caller using third generation sequencing
total releases 6most recent commit 3 months ago
Sars Cov 2_sequencing ⭐ 316
A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.
most recent commit a month ago
Isobar ⭐ 282
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.
total releases 3most recent commit 11 days ago
Shasta ⭐ 258
De novo assembly from Oxford Nanopore reads.
most recent commit 11 days ago
Snap ⭐ 254
Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
most recent commit 5 months ago
Elprep ⭐ 253
elPrep: a high-performance tool for analyzing sequence alignment/map files in sequencing pipelines.
total releases 11most recent commit 2 months ago
Medaka ⭐ 246
Sequence correction provided by ONT Research
total releases 71most recent commit 15 days ago
Nanoplot ⭐ 237
Plotting scripts for long read sequencing data
dependent packages 2total releases 145most recent commit a month agopypi NanoPlot} Downloads
Comp Genomics Class ⭐ 236
Code and examples for JHU Computational Genomics class
most recent commit 9 months ago
Htsjdk ⭐ 236
A Java API for high-throughput sequencing data (HTS) formats.
dependent packages 82total releases 70most recent commit a month ago
Sequenceserver ⭐ 236
Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)
total releases 65most recent commit 21 days ago
Fgbio ⭐ 233
Tools for working with genomic and high throughput sequencing data.
total releases 15most recent commit 25 days ago
Fastqc ⭐ 228
A quality control analysis tool for high throughput sequencing data
most recent commit 25 days ago
Snapatac ⭐ 227
Analysis Pipeline for Single Cell ATAC-seq
most recent commit 4 months ago
Roary ⭐ 219
Rapid large-scale prokaryote pan genome analysis
total releases 83most recent commit 2 months ago
Manta ⭐ 215
Structural variant and indel caller for mapped sequencing data
most recent commit 3 years ago
Mixcr ⭐ 194
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.
most recent commit 8 hours ago
Wgsim ⭐ 188
Reads simulator
most recent commit 10 months ago
Serratus ⭐ 188
Ultra-deep search for novel viruses
most recent commit a month ago
Snp Sites ⭐ 173
Finds SNP sites from a multi-FASTA alignment file
most recent commit 2 years ago
Sarek ⭐ 171
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
most recent commit 14 days ago
Hgvs ⭐ 169
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
dependent packages 10total releases 101most recent commit a month agopypi hgvs} Downloads
Kubegene ⭐ 169
KubeGene - A turn-key Genome Sequencing workflow management framework
most recent commit 2 years ago
Artemis ⭐ 163
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
most recent commit 3 months ago
Splatter ⭐ 161
Simple simulation of single-cell RNA sequencing data
most recent commit 2 months ago
Tram ⭐ 159
Cross-browser CSS3 transitions in JavaScript.
dependent packages 3total releases 18most recent commit 6 years agonpm tram} Downloads
Afterqc ⭐ 157
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
most recent commit 5 years ago
Miso Lims ⭐ 157
MISO: An open-source LIMS for NGS sequencing centres
most recent commit a day ago
Soapdenovo2 ⭐ 156
Next generation sequencing reads de novo assembler.
most recent commit a year ago
Hapcut2 ⭐ 155
software tools for haplotype assembly from sequence data
most recent commit 2 months ago
Mercury ⭐ 153
A minimal and human-readable language and environment for the live coding of algorithmic electronic music.
most recent commit 6 hours ago
Ugene ⭐ 150
UGENE is free open-source cross-platform bioinformatics software
most recent commit 15 hours ago
Laravel Eloquent Sequencer ⭐ 147
A package that allows you to create and manage sequences on Eloquent models.
total releases 13most recent commit 8 months ago
Pycoqc ⭐ 144
pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)
total releases 50most recent commit 5 months ago
Circlator ⭐ 143
A tool to circularize genome assemblies
total releases 33most recent commit 8 months ago
Genomics ⭐ 143
A collection of scripts and notes related to genomics and bioinformatics
most recent commit 2 months ago
Clairvoyante ⭐ 142
Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
most recent commit 2 years ago
Minion_qc ⭐ 141
Quality control for MinION sequencing data
most recent commit a year ago
Crispresso2 ⭐ 139
Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments
most recent commit 12 days ago
Sunbeam ⭐ 138
A robust, extensible metagenomics pipeline
most recent commit 7 days ago
Genomescope ⭐ 135
Fast genome analysis from unassembled short reads
most recent commit 9 months ago
Tcga_example ⭐ 135
most recent commit 3 years ago
Rnaseq Workflow ⭐ 133
A repository for setting up a RNAseq workflow
most recent commit 5 years ago
Nextclade ⭐ 133
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
total releases 50most recent commit 2 days ago
Emp ⭐ 132
Code repository of the Earth Microbiome Project.
most recent commit 21 days ago
Tradeseq ⭐ 132
TRAjectory-based Differential Expression analysis for SEQuencing data
most recent commit 3 months ago
Alignment And Variant Calling Tutorial ⭐ 130
basic walk-throughs for alignment and variant calling from NGS sequencing data
most recent commit 3 years ago
Sccatch ⭐ 128
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
total releases 2most recent commit 2 months ago
Smudgeplot ⭐ 126
Inference of ploidy and heterozygosity structure using whole genome sequencing data
most recent commit 4 months ago
Game Programming Patterns Cn ⭐ 124
游戏编程模式中文
most recent commit 8 years ago
Dragonstar2019 ⭐ 122
most recent commit 3 years ago
D4 Format ⭐ 120
The D4 Quantitative Data Format
dependent packages 3total releases 21most recent commit 5 days agocargo d4-hts} Downloads
Timingsrc ⭐ 118
Source code for timing related libraries managed by webtiming (multi-device timing CG)
most recent commit 2 months ago
Scobot ⭐ 117
SCORM API for Content. JavaScript library, QUnit tests and examples.
most recent commit 2 years ago
Metaphlan ⭐ 115
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
total releases 14most recent commit 20 days ago
Genomicsqlite ⭐ 114
Genomics Extension for SQLite
total releases 18most recent commit 3 months ago
Cellbender ⭐ 113
CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
most recent commit 12 days ago
Ariba ⭐ 112
Antimicrobial Resistance Identification By Assembly
dependent packages 1total releases 54most recent commit 6 months agopypi ariba} Downloads
Sequana ⭐ 112
Sequana: a set of Snakemake NGS pipelines
total releases 75most recent commit 4 days ago
Canvas ⭐ 110
Canvas - Copy number variant (CNV) calling from DNA sequencing data
most recent commit 3 years ago
Crispresso ⭐ 110
Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data
total releases 51most recent commit 3 years ago
Ngstools ⭐ 109
Programs to analyse NGS data for population genetics purposes
most recent commit 2 years ago
Deepbinner ⭐ 108
a signal-level demultiplexer for Oxford Nanopore reads
most recent commit a year ago
Optitype ⭐ 106
Precision HLA typing from next-generation sequencing data
most recent commit 2 years ago
Alfred ⭐ 104
BAM Statistics, Feature Counting and Annotation
most recent commit a month ago
Vdjtools ⭐ 100
Post-analysis of immune repertoire sequencing data
most recent commit 4 months ago
Hts ⭐ 100
biogo high throughput sequencing repository
dependent packages 53total releases 15most recent commit 8 months ago
Msisensor ⭐ 99
microsatellite instability detection using tumor only or paired tumor-normal data
most recent commit a year ago
Nextpolish ⭐ 99
Fast and accurately polish the genome generated by long reads.
most recent commit 9 months ago
Gatk4 Data Processing ⭐ 99
Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools
most recent commit 8 months ago
Cloops ⭐ 99
Accurate and flexible loops calling tool for 3D genomic data.
most recent commit 2 months ago
Facets ⭐ 98
Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
most recent commit 9 months ago
Dna Seq Analysis ⭐ 98
DNA sequencing analysis notes from Ming Tang
most recent commit a year ago
Seq2science ⭐ 97
Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
most recent commit 18 days ago
Decontam ⭐ 93
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
most recent commit a year ago
Awesome Vdj ⭐ 92
Tools and databases for analyzing HLA and VDJ genes.
most recent commit a month ago
Insilicoseq ⭐ 92
🚀 A sequencing simulator
dependent packages 1total releases 36most recent commit 9 months agopypi InSilicoSeq} Downloads
1-100 of 2,265 projects
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