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Search results for variants genomics
genomics
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variants
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16 search results found
Deepvariant
⭐
2,978
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Vg
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1,022
tools for working with genome variation graphs
Adam
⭐
966
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
Snippy
⭐
408
✂️ ⚡ Rapid haploid variant calling and core genome alignment
Maftools
⭐
400
Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
Vcfanno
⭐
334
annotate a VCF with other VCFs/BEDs/tabixed files
Sarek
⭐
299
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Octopus
⭐
285
Bayesian haplotype-based mutation calling
Hap.py
⭐
283
Haplotype VCF comparison tools
Rtg Tools
⭐
260
RTG Tools: Utilities for accurate VCF comparison and manipulation
Hgvs
⭐
226
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
Vcfr
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225
Tools to work with variant call format files
Slivar
⭐
221
genetic variant expressions, annotation, and filtering for great good.
Ga4gh Schemas
⭐
213
Models and APIs for Genomic data. RETIRED 2018-01-24
Exomiser
⭐
174
A Tool to Annotate and Prioritize Exome Variants
Smoove
⭐
173
structural variant calling and genotyping with existing tools, but, smoothly.
Souporcell
⭐
134
Clustering scRNAseq by genotypes
Readthedocs
⭐
133
Documentation for the Google Genomics cookbook.
Assemblytics
⭐
124
Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.
Benchmarking Tools
⭐
110
Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
Open Cravat
⭐
98
A modular annotation tool for genomic variants
Ga4gh Server
⭐
95
Reference implementation of the APIs defined in ga4gh-schemas. RETIRED 2018-01-24
Fermikit
⭐
91
De novo assembly based variant calling pipeline for Illumina short reads
Genomicsdb
⭐
88
High performance data storage for importing, querying and transforming variants.
Mccortex
⭐
86
De novo genome assembly and multisample variant calling
Tiledb Vcf
⭐
79
Efficient variant-call data storage and retrieval library using the TileDB storage library.
Svtyper
⭐
78
Bayesian genotyper for structural variants
Callings Nf
⭐
76
GATK RNA-Seq Variant Calling in Nextflow
Dysgu
⭐
75
Toolkit for calling structural variants using short or long reads
Duphold
⭐
73
don't get DUP'ed or DEL'ed by your putative SVs.
Wrangling Genomics
⭐
62
Data Wrangling and Processing for Genomics
Hla
⭐
57
xHLA: Fast and accurate HLA typing from short read sequence data
Getting Started Bigquery
⭐
51
Examples of how to get started with genomics data in BigQuery in many languages.
Teamteri
⭐
50
Genomics (computational bioinformatic data analysis) running on GCP, AWS or Azure
Rare Disease Wf
⭐
49
(WIP) best-practices workflow for rare disease
Bactmap
⭐
45
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
Googlegenomics
⭐
44
An R package for Google Genomics API queries.
Pandas Genomics
⭐
42
Pandas ExtensionDtypes for dealing with genomics data
Hts Nim Tools
⭐
41
useful command-line tools written to show-case hts-nim
Lrsim
⭐
38
10x Genomics Reads Simulator
Chm Eval
⭐
37
Variantkey
⭐
34
Numerical Encoding for Human Genetic Variants
Bio Dockers
⭐
32
🐳 Bio-dockers: dockerized bioinformatic tools
Mtbseq_source
⭐
32
MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.
Grocsvs
⭐
32
Genome-wide reconstruction of complex structural variants
Specification
⭐
32
GA4GH Beacon specification.
Mindthegap
⭐
30
MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool.
Cerebra
⭐
26
A tool for fast and accurate summarizing of variant calling format (VCF) files
Varsome Api Client Python
⭐
26
Example client programs for Saphetor's VarSome annotation API
Cutevcf
⭐
23
simple viewer for variant call format using htslib
Samovar
⭐
22
Somatic (mosaic) SNV caller for 10X Genomics data using random forest classification and feature-based filters
Cmdbtools
⭐
21
Command line tools for CMDB varaints browser
Genomeanalysismodule
⭐
21
Welcome to the website and github repository for the Genome Analysis Module. This website will guide the learning experience for trainees in the UBC MSc Genetic Counselling Training Program, as they embark on a journey to learn about analyzing genomes.
Vcf2fhir
⭐
20
vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration
Smcounter
⭐
18
smCounter: a versatile UMI-aware variant caller to detect both somatic and germline SNVs and indels. Published in article "Detecting very low allele fraction variants using targeted DNA sequencing and a novel molecular barcode-aware variant caller", BMC Genomics, 2017 18:5. https://bmcgenomics.biomedcentral.com/articles/10.
Clairs To
⭐
18
ClairS-TO - a deep-learning method for tumor-only somatic SNV calling
Icallsv
⭐
16
A Framework to call Structural Variants from NGS based datasets
Spark Vcf
⭐
15
Spark VCF data source implementation for Dataframes
Svaha2
⭐
14
Linear-time, low-memory construction of variation graphs
Variantdb_challenge
⭐
14
Finding a scalable alternative to the VCF File for genomics analysis
Mitty
⭐
13
Seven Bridges Genomics aligner/caller debugging and analysis tools
Misc Genomics Tools
⭐
13
assorted scripts for doing genomics
Gnomad_python_api
⭐
13
🧬 gnomAD Python API is used to obtain data from gnomAD (genome aggregation database).
Falcon Genome
⭐
13
Falcon Accelerated Genomics Pipelines
Seave
⭐
12
Seave is a web platform that enables genetic variants to be easily filtered and annotated with in silico pathogenicity prediction scores and annotations from popular disease databases. Seave stores genomic variation of all types and sizes, and allows filtering for specific inheritance patterns, quality values, allele frequencies and gene lists. Seave is open source and deployable locally, or on a cloud computing provider, and works readily with gene panel, exome and whole genome data, scaling fr
Deepvariant On Spark
⭐
11
DeepVariant-on-Spark is a germline short variant calling pipeline that runs Google DeepVariant on Apache Spark at scale.
Genetics Docs
⭐
10
Algebra
⭐
10
A Boolean Algebra for Genetic Variants
Exoseq
⭐
10
Please consider using/contributing to https://github.com/nf-core/sarek
Topsorter
⭐
10
Graphical assessment of structrial variants using 10x genomics data
Application
⭐
9
Development build for SMART Cancer Navigator
Sopang
⭐
9
SOPanG, a simple tool for pattern matching over an elastic-degenerate string, a recently proposed simplified model for the pan-genome.
Jarvis
⭐
9
JARVIS: a comprehensive deep learning framework to prioritise non-coding variants in whole genomes
Quantumclone
⭐
8
Clonal reconstruction from HTS data
Bigquery Genomics Qc
⭐
7
Genomics QC pipeline
Mgp1000
⭐
7
Nextflow bioinformatics pipeline for large-scale analysis of Multiple Myeloma genomes
Varathon
⭐
7
A scalable variant calling and benchmarking framework supporting both short and long reads.
2019genomicsepidemiologyworkshop
⭐
6
2019 Genomics Epidemiology Workshop at Academia Sinica
Sv Pop
⭐
6
Upscaling SV detection to a multi-population level.
Clinvar Kaggle
⭐
6
Scripts related to the ClinVar conflicting classifications dataset on Kaggle
Fings
⭐
6
Filters for Next Generation Sequencing
Virtual Normal Correction
⭐
6
Set of commandline tools for analysis of tumor variants without a matching normal. Method described in Genome Research: http://genome.cshlp.org/content/25/9/1382.full
Tersect
⭐
6
Command-line utility for conducting fast set theoretical operations and genetic distance estimation on biological sequence variant data.
Python Outbreak Info
⭐
5
Python package to access the genomics and epidemiology data and Research Library metadata compiled and standardized on outbreak.info
Eva
⭐
5
Efficient Variant Analysis
Tutorials
⭐
5
bioinformatics tutorials
Variantkey Nim
⭐
5
nim-wrapper for variantkey -- (chrom, pos, ref, alt) -> uint64
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