Illumina

Illumina Open Source Software

Pinned Repositories

canvas
Canvas - Copy number variant (CNV) calling from DNA sequencing data
Language:C#120 24 13420
DRAGMAP
DRAGEN open-source mapper
Language:C++148 19 5428
ExpansionHunter
A tool for estimating repeat sizes
Language:C++173 30 11153
hap.py
Haplotype VCF comparison tools
Language:C++396 43 167119
manta
Structural variant and indel caller for mapped sequencing data
Language:C++388 41 302150
Nirvana
The nimble & robust variant annotator
Language:C#166 32 11744
paragraph
Graph realignment tools for structural variants
Language:C++145 20 6928
pyflow
A lightweight parallel task engine
Language:Python143 31 2344
SpliceAI
A deep learning-based tool to identify splice variants
Language:Python375 20 133155
strelka
Strelka2 germline and somatic small variant caller
Language:C++350 29 237102

Illumina's Repositories

Illumina/hap.py
Haplotype VCF comparison tools
Language:C++396 43 167119
Illumina/manta
Structural variant and indel caller for mapped sequencing data
Language:C++388 41 302150
Illumina/SpliceAI
A deep learning-based tool to identify splice variants
Language:Python375 20 133155
Illumina/ExpansionHunter
A tool for estimating repeat sizes
Language:C++173 30 11153
Illumina/Nirvana
The nimble & robust variant annotator
Language:C#166 32 11744
Illumina/DRAGMAP
DRAGEN open-source mapper
Language:C++148 19 5428
Illumina/paragraph
Graph realignment tools for structural variants
Language:C++145 20 6928
Illumina/Pisces
Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
Language:C#91 21 7116
Illumina/ExpansionHunterDenovo
A suite of tools for detecting expansions of short tandem repeats
Language:C++76 15 4525
Illumina/interop
C++ Library to parse Illumina InterOp files
Language:C++75 22 17226
Illumina/REViewer
A tool for visualizing alignments of reads in regions containing tandem repeats
Language:C++72 14 4713
Illumina/akt
Ancestry and Kinship Tools
Language:C++67 11 2212
Illumina/PrimateAI-3D
Language:Python55 16 49
Illumina/SMNCopyNumberCaller
A copy number caller for SMN1 and SMN2 to enable SMA diagnosis and carrier screening with WGS
Language:Python49 10 1012
Illumina/BeadArrayFiles
Python library to parse file formats related to Illumina bead arrays
Language:Python45 19 1934
Illumina/Cyrius
A tool to genotype CYP2D6 with WGS data
Language:Python45 11 365
Illumina/GTCtoVCF
Script to convert GTC/BPM files to VCF
Language:Python40 20 4630
Illumina/witty.er
What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.
Language:C#26 5 71
Illumina/Gauchian
A variant caller for the GBA gene using WGS data
Language:Python19 15 33
Illumina/zippy
The ZIPPY pipeline prototyping system
Language:Python5 5 24
Illumina/ica-sdk-python
Language:Python4
Illumina/NirvanaDocumentation
Language:MDX4 7 14
Illumina/dragen-azure-quickstart
Language:HTML3 7 1
Illumina/NeoMutalyzer
Inspired by Mutalyzer and frustrated by RefSeq, we created this transcript annotation validator
Language:C#3 8 00
Illumina/BlockCompression
Block compression library used by Nirvana
Language:C++2 4 01
Illumina/licenses
2 7 282
Illumina/Pelops
Language:Python2 8 01
Illumina/dragen-aws-batch-quickstart
Language:HTML1 7 0
Illumina/IlluminaConnectedAnnotationsDocumentation
Language:MDX01
Illumina/minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
Language:C1 0