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The Top 23 Sequencing Open Source Projects

Open source projects categorized as Sequencing
Categories > Science > Sequencing
Deepvariant ⭐ 2,978
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
Fastp ⭐ 1,602
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging.
total releases 1most recent commit 6 months ago
Gatk ⭐ 1,576
Official code repository for GATK versions 4 and up
dependent packages 2total releases 46most recent commit a month ago
Samtools ⭐ 1,496
Tools (written in C using htslib) for manipulating next-generation sequencing data
most recent commit 3 months ago
Ncov ⭐ 1,348
Nextstrain build for novel coronavirus SARS-CoV-2
most recent commit 3 months ago
Galaxy ⭐ 1,211
Data intensive science for everyone.
dependent packages 23total releases 30most recent commit 3 months agopypi galaxy-util} Downloads
Getting Started With Genomics Tools And Resources ⭐ 991
Unix, R and python tools for genomics and data science
most recent commit 3 months ago
Adam ⭐ 966
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 3 months ago
Picard ⭐ 914
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 176most recent commit 3 months ago
Rnaseq ⭐ 718
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
most recent commit 3 months ago
Mosdepth ⭐ 617
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
most recent commit 5 months ago
Rna Seq Analysis ⭐ 614
RNAseq analysis notes from Ming Tang
most recent commit 2 years ago
Scrnaseq Analysis Notes ⭐ 540
scRNAseq analysis notes from Ming Tang
most recent commit 4 months ago
Phyloseq ⭐ 520
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 6 months ago
Uncalled ⭐ 507
Raw nanopore signal mapper that enables real-time targeted sequencing
most recent commit 4 months ago
Fetch ⭐ 493
Simple & Efficient data access for Scala and Scala.js
dependent packages 7total releases 25most recent commit a month ago
Sniffles ⭐ 479
Structural variation caller using third generation sequencing
total releases 8most recent commit 3 months ago
Cutadapt ⭐ 475
Cutadapt removes adapter sequences from sequencing reads
dependent packages 24total releases 64most recent commit 3 months agopypi cutadapt} Downloads
Cnvkit ⭐ 435
Copy number variant detection from targeted DNA sequencing
total releases 50most recent commit 4 months ago
Fastqc ⭐ 362
A quality control analysis tool for high throughput sequencing data
most recent commit 3 months ago
Medaka ⭐ 359
Sequence correction provided by ONT Research
total releases 85most recent commit 4 months ago
Isobar ⭐ 348
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 4most recent commit 3 months ago
Hisat2 ⭐ 345
Graph-based alignment (Hierarchical Graph FM index)
most recent commit 2 years ago
The 10 Most Depended On Sequencing Open Source Projects
Htsjdk ⭐ 271
A Java API for high-throughput sequencing data (HTS) formats.
dependent packages 87total releases 78latest release October 13, 2023most recent commit 4 months ago
Hts ⭐ 115
biogo high throughput sequencing repository
dependent packages 71total releases 16latest release August 21, 2022most recent commit 8 months ago
Temporal ⭐ 79
Non-blocking, temporal task sequencing. For use with robots built with Johnny-Five
dependent packages 36total releases 26latest release August 08, 2018most recent commit 6 years agonpm temporal} Downloads
Cutadapt ⭐ 475
Cutadapt removes adapter sequences from sequencing reads
dependent packages 24total releases 64latest release December 06, 2023most recent commit 3 months agopypi cutadapt} Downloads
Galaxy ⭐ 1,211
Data intensive science for everyone.
dependent packages 23total releases 30latest release December 08, 2023most recent commit 3 months agopypi galaxy-util} Downloads
Graph Sequencer ⭐ 18
Sort items in a graph using a topological sort while resolving cycles with priority groups
dependent packages 15total releases 2latest release December 07, 2017most recent commit 4 years agonpm graph-sequencer} Downloads
Hgvs ⭐ 226
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
dependent packages 12total releases 104latest release November 21, 2022most recent commit 3 months agopypi hgvs} Downloads
Picard ⭐ 914
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 176latest release November 14, 2023most recent commit 3 months ago
Biocommons.seqrepo ⭐ 34
non-redundant, compressed, journalled, file-based storage for biological sequences
dependent packages 12total releases 42latest release November 13, 2023most recent commit 3 months agopypi biocommons.seqrepo} Downloads
The 10 Latest Releases In Sequencing Open Source Projects
Galaxy ⭐ 1,211
Data intensive science for everyone.
dependent packages 23total releases 30latest release December 08, 2023most recent commit 3 months agopypi galaxy-util} Downloads
Sequana ⭐ 136
Sequana: a set of Snakemake NGS pipelines
dependent packages 8total releases 90latest release December 06, 2023most recent commit 3 months agopypi sequana} Downloads
Cutadapt ⭐ 475
Cutadapt removes adapter sequences from sequencing reads
dependent packages 24total releases 64latest release December 06, 2023most recent commit 3 months agopypi cutadapt} Downloads
Medaka ⭐ 359
Sequence correction provided by ONT Research
total releases 85latest release December 06, 2023most recent commit 4 months ago
Kairos ⭐ 120
A complete framework for data control and composition in the vvvv visual programming environment.
dependent packages 1total releases 14latest release December 02, 2023most recent commit 5 months agonuget VL.Kairos.Runtime} Downloads
Geofetch ⭐ 33
Builds a PEP from SRA or GEO accessions
total releases 21latest release November 29, 2023most recent commit 5 months ago
Rnalysis ⭐ 114
RNA sequencing analysis software
total releases 43latest release November 22, 2023most recent commit 3 months ago
Picard ⭐ 914
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 176latest release November 14, 2023most recent commit 3 months ago
Biocommons.seqrepo ⭐ 34
non-redundant, compressed, journalled, file-based storage for biological sequences
dependent packages 12total releases 42latest release November 13, 2023most recent commit 3 months agopypi biocommons.seqrepo} Downloads
Popular Science Categories
Physics
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