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The Top 23 Sequencing Open Source Projects

Open source projects categorized as Sequencing
Categories > Science > Sequencing
Deepvariant ⭐ 2,828
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
most recent commit 2 days ago
Fastp ⭐ 1,515
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging.
total releases 1most recent commit 8 days ago
Gatk ⭐ 1,442
Official code repository for GATK versions 4 and up
dependent packages 2total releases 44most recent commit a day ago
Samtools ⭐ 1,382
Tools (written in C using htslib) for manipulating next-generation sequencing data
most recent commit 3 days ago
Ncov ⭐ 1,339
Nextstrain build for novel coronavirus SARS-CoV-2
most recent commit 2 days ago
Galaxy ⭐ 1,109
Data intensive science for everyone.
dependent packages 12total releases 13most recent commit 18 hours agopypi galaxy-util} Downloads
Adam ⭐ 946
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 4 months ago
Getting Started With Genomics Tools And Resources ⭐ 872
Unix, R and python tools for genomics and data science
most recent commit 3 months ago
Picard ⭐ 871
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 172most recent commit 5 days ago
Htslib ⭐ 694
C library for high-throughput sequencing data formats
dependent packages 1total releases 9most recent commit 2 days agocargo hts-sys} Downloads
Rnaseq ⭐ 622
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
most recent commit 6 days ago
Rna Seq Analysis ⭐ 614
RNAseq analysis notes from Ming Tang
most recent commit 2 years ago
Deeptools ⭐ 573
Tools to process and analyze deep sequencing data.
most recent commit 7 days ago
Mosdepth ⭐ 547
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
most recent commit 3 months ago
Uncalled ⭐ 504
Raw nanopore signal mapper that enables real-time targeted sequencing
most recent commit 2 days ago
Fetch ⭐ 490
Simple & Efficient data access for Scala and Scala.js
most recent commit 3 days ago
Phyloseq ⭐ 456
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 ⭐ 451
scRNAseq analysis notes from Ming Tang
most recent commit 15 days ago
Cutadapt ⭐ 443
Cutadapt removes adapter sequences from sequencing reads
most recent commit 13 days ago
Cnvkit ⭐ 402
Copy number variant detection from targeted DNA sequencing
total releases 49most recent commit 3 months ago
Sniffles ⭐ 363
Structural variation caller using third generation sequencing
total releases 7most recent commit 8 months ago
Hisat2 ⭐ 345
Graph-based alignment (Hierarchical Graph FM index)
most recent commit a year ago
Sars Cov 2_sequencing ⭐ 333
A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.
most recent commit 2 months ago
The 10 Most Depended On Sequencing Open Source Projects
Htsjdk ⭐ 259
A Java API for high-throughput sequencing data (HTS) formats.
dependent packages 82total releases 74latest release November 23, 2022most recent commit 3 months ago
Galaxy ⭐ 1,109
Data intensive science for everyone.
dependent packages 12total releases 13latest release November 02, 2021most recent commit 18 hours agopypi galaxy-util} Downloads
Hgvs ⭐ 207
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
dependent packages 11total releases 104latest release November 21, 2022most recent commit 15 days agopypi hgvs} Downloads
D4 Format ⭐ 135
The D4 Quantitative Data Format
dependent packages 4total releases 22latest release August 15, 2022most recent commit 4 months agocargo d4-hts} Downloads
Tram ⭐ 159
Cross-browser CSS3 transitions in JavaScript.
dependent packages 3total releases 18latest release December 16, 2016most recent commit 6 years agonpm tram} Downloads
Nanoplot ⭐ 305
Plotting scripts for long read sequencing data
dependent packages 2total releases 145latest release April 07, 2022most recent commit 6 days agopypi NanoPlot} Downloads
Gatk ⭐ 1,442
Official code repository for GATK versions 4 and up
dependent packages 2total releases 44latest release April 13, 2022most recent commit a day ago
Ariba ⭐ 135
Antimicrobial Resistance Identification By Assembly
dependent packages 1total releases 54latest release September 07, 2020most recent commit 13 days agopypi ariba} Downloads
The 10 Latest Releases In Sequencing Open Source Projects
Kairos ⭐ 112
A complete framework for data control and composition in the vvvv visual programming environment.
dependent packages 1total releases 6latest release January 19, 2023most recent commit 14 days agonuget VL.AlchemX} Downloads
Htsjdk ⭐ 259
A Java API for high-throughput sequencing data (HTS) formats.
dependent packages 82total releases 74latest release November 23, 2022most recent commit 3 months ago
Hgvs ⭐ 207
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
dependent packages 11total releases 104latest release November 21, 2022most recent commit 15 days agopypi hgvs} Downloads
Sccatch ⭐ 171
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
total releases 4latest release November 07, 2022most recent commit a month ago
D4 Format ⭐ 135
The D4 Quantitative Data Format
dependent packages 4total releases 22latest release August 15, 2022most recent commit 4 months agocargo d4-hts} Downloads
Sequana ⭐ 123
Sequana: a set of Snakemake NGS pipelines
total releases 77latest release July 01, 2022most recent commit a month ago
Medaka ⭐ 308
Sequence correction provided by ONT Research
total releases 74latest release June 20, 2022most recent commit 21 days ago
Gatk ⭐ 1,442
Official code repository for GATK versions 4 and up
dependent packages 2total releases 44latest release April 13, 2022most recent commit a day ago
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