Illumina/PrimateAI-3D

Language: Python - Size: 28.4 MB - Last synced: about 18 hours ago - Pushed: 1 day ago - Stars: 55 - Forks: 9

Illumina/SpliceAI

A deep learning-based tool to identify splice variants

Language: Python - Size: 17.9 MB - Last synced: 21 days ago - Pushed: 2 months ago - Stars: 368 - Forks: 152

Illumina/IlluminaConnectedAnnotationsDocumentation

Language: MDX - Size: 51.2 MB - Last synced: 30 days ago - Pushed: 30 days ago - Stars: 0 - Forks: 1

Illumina/Nirvana

The nimble & robust variant annotator

Language: C# - Size: 105 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 164 - Forks: 43

Illumina/manta 📦

Structural variant and indel caller for mapped sequencing data

Language: C++ - Size: 113 MB - Last synced: 21 days ago - Pushed: over 1 year ago - Stars: 388 - Forks: 151

Illumina/interop

C++ Library to parse Illumina InterOp files

Language: C++ - Size: 21.5 MB - Last synced: 9 days ago - Pushed: 6 months ago - Stars: 75 - Forks: 26

Illumina/dragen-aws-batch-quickstart

Language: HTML - Size: 1.5 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 1 - Forks: 0

Illumina/SlimCache

Nirvana tool that creates RefSeq- or Ensembl-specific cache files

Language: C# - Size: 62.5 KB - Last synced: 2 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

Illumina/agg 📦

gvcf aggregation tool

Size: 5.58 MB - Last synced: 2 months ago - Pushed: over 6 years ago - Stars: 12 - Forks: 3

Illumina/MarViN

Language: C++ - Size: 5.82 MB - Last synced: 2 months ago - Pushed: about 7 years ago - Stars: 5 - Forks: 2

Illumina/ica-sdk-python

Language: Python - Size: 1.44 MB - Last synced: 2 months ago - Pushed: 6 months ago - Stars: 4 - Forks: 0

Illumina/Isaac3

Aligner for sequencing data

Language: C++ - Size: 86.1 MB - Last synced: 2 months ago - Pushed: over 6 years ago - Stars: 18 - Forks: 2

Illumina/GffCreator

Creates GFF files from Nirvana cache files

Language: C# - Size: 65.4 KB - Last synced: 2 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

Illumina/CacheUtils

Creates new Nirvana gene & transcript cache files

Size: 13.7 KB - Last synced: 2 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

Illumina/DRAGMAP

DRAGEN open-source mapper

Language: C++ - Size: 12 MB - Last synced: 2 months ago - Pushed: 9 months ago - Stars: 145 - Forks: 28

Illumina/BamMetrics

Efficient and accurate metrics from aligned reads - mismatch rate, percent proper pairs, etc.

Size: 0 Bytes - Last synced: 2 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

Illumina/isaac2

Aligner for sequencing data

Language: C++ - Size: 202 MB - Last synced: 2 months ago - Pushed: about 8 years ago - Stars: 21 - Forks: 4

Illumina/BlockCompression

Block compression library used by Nirvana

Language: C++ - Size: 68.4 KB - Last synced: 2 months ago - Pushed: over 1 year ago - Stars: 2 - Forks: 1

Illumina/licenses

Size: 27.3 KB - Last synced: 2 months ago - Pushed: 5 months ago - Stars: 2 - Forks: 83

Illumina/GTCtoVCF

Script to convert GTC/BPM files to VCF

Language: Python - Size: 788 KB - Last synced: 2 months ago - Pushed: 3 months ago - Stars: 40 - Forks: 29

Illumina/ExpansionHunter

A tool for estimating repeat sizes

Language: C++ - Size: 9.35 MB - Last synced: 2 months ago - Pushed: 4 months ago - Stars: 165 - Forks: 51

Illumina/pyflow

A lightweight parallel task engine

Language: Python - Size: 2.7 MB - Last synced: 2 months ago - Pushed: almost 4 years ago - Stars: 139 - Forks: 44

Illumina/GraphAlignmentViewer

Language: Python - Size: 738 KB - Last synced: 2 months ago - Pushed: over 2 years ago - Stars: 32 - Forks: 10

Illumina/RepeatCatalogs

Size: 36.5 MB - Last synced: 2 months ago - Pushed: over 2 years ago - Stars: 14 - Forks: 2

Illumina/ExpansionHunterDenovo

A suite of tools for detecting expansions of short tandem repeats

Language: C++ - Size: 3.88 MB - Last synced: 2 months ago - Pushed: 11 months ago - Stars: 72 - Forks: 24

Illumina/REViewer

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

Language: C++ - Size: 167 MB - Last synced: 2 months ago - Pushed: 5 months ago - Stars: 69 - Forks: 12

Illumina/hap.py

Haplotype VCF comparison tools

Language: C++ - Size: 177 MB - Last synced: 2 months ago - Pushed: 6 months ago - Stars: 388 - Forks: 119

Illumina/strelka

Strelka2 germline and somatic small variant caller

Language: C++ - Size: 220 MB - Last synced: 2 months ago - Pushed: over 2 years ago - Stars: 342 - Forks: 100

Illumina/canvas 📦

Canvas - Copy number variant (CNV) calling from DNA sequencing data

Language: C# - Size: 363 MB - Last synced: 2 months ago - Pushed: over 4 years ago - Stars: 119 - Forks: 20

Illumina/Polaris

Data and information about the Polaris study

Size: 71.2 MB - Last synced: 2 months ago - Pushed: over 4 years ago - Stars: 51 - Forks: 8

Illumina/dragen-azure-quickstart

Language: HTML - Size: 694 KB - Last synced: 2 months ago - Pushed: 9 months ago - Stars: 3 - Forks: 0

Illumina/NeoMutalyzer

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

Language: C# - Size: 1.43 MB - Last synced: 2 months ago - Pushed: about 2 years ago - Stars: 3 - Forks: 0

Illumina/NirvanaDocumentation

Language: MDX - Size: 67 MB - Last synced: 2 months ago - Pushed: 3 months ago - Stars: 4 - Forks: 4

Illumina/Cyrius

A tool to genotype CYP2D6 with WGS data

Language: Python - Size: 5.1 MB - Last synced: 13 days ago - Pushed: 8 months ago - Stars: 44 - Forks: 5

Illumina/SMNCopyNumberCaller

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

Language: Python - Size: 3.74 MB - Last synced: 2 months ago - Pushed: 8 months ago - Stars: 46 - Forks: 13

Illumina/happyR

R tools to interact with hap.py output

Language: R - Size: 60 MB - Last synced: 2 months ago - Pushed: almost 5 years ago - Stars: 15 - Forks: 1

Illumina/happyCompare 📦

Reporting toolbox for happy output

Language: R - Size: 105 MB - Last synced: 2 months ago - Pushed: almost 5 years ago - Stars: 7 - Forks: 4

Illumina/Pisces

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

Language: C# - Size: 96.8 MB - Last synced: 2 months ago - Pushed: almost 2 years ago - Stars: 91 - Forks: 16

Illumina/paragraph

Graph realignment tools for structural variants

Language: C++ - Size: 30.8 MB - Last synced: 2 months ago - Pushed: over 1 year ago - Stars: 143 - Forks: 28

Illumina/PrimateAI

deep residual neural network for classifying the pathogenicity of missense mutations.

Language: Python - Size: 345 KB - Last synced: 2 months ago - Pushed: almost 3 years ago - Stars: 110 - Forks: 30

Illumina/Pelops

Language: Python - Size: 1.81 MB - Last synced: 11 days ago - Pushed: 4 months ago - Stars: 1 - Forks: 1

Illumina/PlatinumGenomes

The Platinum Genomes Truthset

Size: 8.79 KB - Last synced: 2 months ago - Pushed: over 6 years ago - Stars: 83 - Forks: 9

Illumina/gvcfgenotyper

A utility for merging and genotyping Illumina-style GVCFs.

Language: C++ - Size: 7.92 MB - Last synced: 2 months ago - Pushed: over 5 years ago - Stars: 31 - Forks: 2

Illumina/BeadArrayFiles

Python library to parse file formats related to Illumina bead arrays

Language: Python - Size: 121 KB - Last synced: 2 months ago - Pushed: 3 months ago - Stars: 42 - Forks: 34

Illumina/akt

Ancestry and Kinship Tools

Language: C++ - Size: 41.4 MB - Last synced: 2 months ago - Pushed: over 1 year ago - Stars: 62 - Forks: 12

Illumina/Isaac4

Isaac aligner version 4

Language: C++ - Size: 110 MB - Last synced: 2 months ago - Pushed: over 2 years ago - Stars: 15 - Forks: 3

Illumina/Gauchian

A variant caller for the GBA gene using WGS data

Language: Python - Size: 3.63 MB - Last synced: 24 days ago - Pushed: 3 months ago - Stars: 18 - Forks: 2

Illumina/tHapMix 📦

Haplotype-based somatic genome simulator

Language: Python - Size: 4.79 MB - Last synced: 2 months ago - Pushed: about 7 years ago - Stars: 10 - Forks: 2

Illumina/witty.er

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

Language: C# - Size: 110 MB - Last synced: 2 months ago - Pushed: 9 months ago - Stars: 26 - Forks: 1

Illumina/minimap2 Fork of lh3/minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Size: 1.39 MB - Last synced: 2 months ago - Pushed: 12 months ago - Stars: 0 - Forks: 0

Illumina/zippy

The ZIPPY pipeline prototyping system

Language: Python - Size: 90.8 KB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 5 - Forks: 4

Illumina/BaseSpace_Clarity_LIMS

API libraries, application examples, and custom tools for BaseSpace Clarity LIMS

Language: Python - Size: 26.4 KB - Last synced: 2 months ago - Pushed: almost 4 years ago - Stars: 15 - Forks: 8

Illumina/novaseq-lims-api

Documentation and tools for users of the NovaSeq LIMS API

Language: C# - Size: 229 KB - Last synced: 2 months ago - Pushed: about 5 years ago - Stars: 3 - Forks: 3