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Illumina

Illumina

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Illumina Open Source Software

Home Page:http://www.illumina.com

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Illumina's repositories

hap.py

Haplotype VCF comparison tools

Language:C++License:NOASSERTIONStargazers:395Issues:43Issues:167

manta

Structural variant and indel caller for mapped sequencing data

Language:C++License:GPL-3.0Stargazers:388Issues:41Issues:302

SpliceAI

A deep learning-based tool to identify splice variants

Language:PythonLicense:NOASSERTIONStargazers:373Issues:20Issues:133

ExpansionHunter

A tool for estimating repeat sizes

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Nirvana

The nimble & robust variant annotator

Language:C#License:GPL-3.0Stargazers:166Issues:32Issues:117

DRAGMAP

DRAGEN open-source mapper

Language:C++License:NOASSERTIONStargazers:149Issues:19Issues:54

paragraph

Graph realignment tools for structural variants

Language:C++License:NOASSERTIONStargazers:145Issues:20Issues:69

Pisces

Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.

Language:C#License:GPL-3.0Stargazers:91Issues:21Issues:71

ExpansionHunterDenovo

A suite of tools for detecting expansions of short tandem repeats

Language:C++License:NOASSERTIONStargazers:75Issues:15Issues:44

interop

C++ Library to parse Illumina InterOp files

Language:C++License:GPL-3.0Stargazers:75Issues:22Issues:172

REViewer

A tool for visualizing alignments of reads in regions containing tandem repeats

Language:C++License:GPL-3.0Stargazers:70Issues:14Issues:47

akt

Ancestry and Kinship Tools

Language:C++License:GPL-3.0Stargazers:65Issues:11Issues:22

PrimateAI-3D

Language:PythonLicense:NOASSERTIONStargazers:55Issues:16Issues:4

SMNCopyNumberCaller

A copy number caller for SMN1 and SMN2 to enable SMA diagnosis and carrier screening with WGS

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BeadArrayFiles

Python library to parse file formats related to Illumina bead arrays

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Cyrius

A tool to genotype CYP2D6 with WGS data

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GTCtoVCF

Script to convert GTC/BPM files to VCF

Language:PythonLicense:Apache-2.0Stargazers:40Issues:20Issues:44

witty.er

What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.

Language:C#License:NOASSERTIONStargazers:26Issues:5Issues:7

Gauchian

A variant caller for the GBA gene using WGS data

Language:PythonLicense:NOASSERTIONStargazers:19Issues:15Issues:3

zippy

The ZIPPY pipeline prototyping system

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ica-sdk-python

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NirvanaDocumentation

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dragen-azure-quickstart

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NeoMutalyzer

Inspired by Mutalyzer and frustrated by RefSeq, we created this transcript annotation validator

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BlockCompression

Block compression library used by Nirvana

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licenses

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dragen-aws-batch-quickstart

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Pelops

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IlluminaConnectedAnnotationsDocumentation

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minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

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