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Search results for bioinformatics variants
bioinformatics
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variants
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17 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.
Awesome Bioinformatics
⭐
2,505
A curated list of awesome Bioinformatics libraries and software.
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
Manta
⭐
333
Structural variant and indel caller for mapped sequencing data
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
Awesome Cancer Variant Databases
⭐
284
A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.
Hap.py
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283
Haplotype VCF comparison tools
Hgvs
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226
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
Strelka
⭐
204
Strelka2 germline and somatic small variant caller
Graphtyper
⭐
156
Population-scale genotyping using pangenome graphs
Clairvoyante
⭐
142
Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
Poplddecay
⭐
138
PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files
Souporcell
⭐
134
Clustering scRNAseq by genotypes
Mutscan
⭐
127
Detect and visualize target mutations by scanning FastQ files directly
Assemblytics
⭐
124
Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.
Dragonstar2019
⭐
122
Variantspark
⭐
121
machine learning for genomic variants
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
Myvariant.info
⭐
84
MyVariant.info: A BioThings API for human variant annotations
Tiledb Vcf
⭐
79
Efficient variant-call data storage and retrieval library using the TileDB storage library.
Svtools
⭐
79
Tools for processing and analyzing structural variants.
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
Clair
⭐
74
Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling
Charger
⭐
70
Characterization of Germline variants
Svviz
⭐
61
Read visualizer for structural variants
Transanno
⭐
54
accurate LiftOver tool for new genome assemblies
Jannovar
⭐
51
Annotation of VCF variants with functional impact and from databases (executable+library)
Teamteri
⭐
50
Genomics (computational bioinformatic data analysis) running on GCP, AWS or Azure
Vembrane
⭐
50
vembrane filters VCF records using python expressions
Mtoolbox
⭐
44
A bioinformatics pipeline to analyze mtDNA from NGS data
Classifycnv
⭐
43
ClassifyCNV: a tool for clinical annotation of copy-number variants
Hts Nim Tools
⭐
41
useful command-line tools written to show-case hts-nim
Seqarray
⭐
41
Data management of large-scale whole-genome sequence variant calls (Development version only)
Ococo
⭐
39
Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.
Lrsim
⭐
38
10x Genomics Reads Simulator
Chm Eval
⭐
37
Iarc Nf
⭐
35
List of IARC bioinformatics nextflow pipelines
Bio Dockers
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32
🐳 Bio-dockers: dockerized bioinformatic tools
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.
Skyhawk
⭐
29
An Artificial Neural Network-based discriminator for validating clinically significant genomic variants
16gt
⭐
26
Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
Varsome Api Client Python
⭐
26
Example client programs for Saphetor's VarSome annotation API
Mutalyzer
⭐
25
Tool suite for HGVS variant descriptions
Cutevcf
⭐
23
simple viewer for variant call format using htslib
Autopvs1
⭐
23
An automatic classification tool for PVS1 interpretation of null variants
G3viz
⭐
21
Lollipop-diagram to interactively visualize genetic mutations
Tagore
⭐
21
The script presents a simple way to visualize features on human chromosome ideograms
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.
Mageri
⭐
19
MAGERI - Assemble, align and call variants for targeted genome re-sequencing with unique molecular identifiers
Clairs To
⭐
18
ClairS-TO - a deep-learning method for tumor-only somatic SNV calling
Svcollector
⭐
17
Method to optimally select samples for validation and resequencing
Icallsv
⭐
16
A Framework to call Structural Variants from NGS based datasets
Pavfinder
⭐
14
🔍 Post Assembly Variants Finder
Mitty
⭐
13
Seven Bridges Genomics aligner/caller debugging and analysis tools
Lava
⭐
13
LAVA: Lightweight Assignment of Variant Alleles
Ngs Pipeline
⭐
12
Pipeline for Somatic Variant Calling with WES and WGS data
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
Ebaii
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12
Supports de cours de l'Ecole de Bioinformatique Aviesan - IFB - Inserm "Initiation au traitement des données de génomique obtenues par séquençage à haut débit"
Pyseqarray
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12
PySeqArray: data manipulation of whole-genome sequencing variants with SeqArray files in Python (pre-release version)
Deepvariant On Spark
⭐
11
DeepVariant-on-Spark is a germline short variant calling pipeline that runs Google DeepVariant on Apache Spark at scale.
Kf Somatic Workflow
⭐
11
🔬 Somatic workflow for Kids-First
Exoseq
⭐
10
Please consider using/contributing to https://github.com/nf-core/sarek
Algebra
⭐
10
A Boolean Algebra for Genetic Variants
Gap2seq
⭐
9
Gap2Seq is a gap filling and insertion genotyping tool.
Sopang
⭐
9
SOPanG, a simple tool for pattern matching over an elastic-degenerate string, a recently proposed simplified model for the pan-genome.
Application
⭐
9
Development build for SMART Cancer Navigator
Variantconvert
⭐
9
A customizable genetic variants file format converter.
Mgp1000
⭐
7
Nextflow bioinformatics pipeline for large-scale analysis of Multiple Myeloma genomes
Convolutional Embedded Networks
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7
Convolutional Embedded Networks for Population Scale Clustering and Bio-ancestry Inferencing
Fonda
⭐
7
Fonda is a framework which offers scalable and automatic analysis of multiple NGS sequencing data types
G3lollipop.js
⭐
7
Lollipop-diagram to visualize genomic mutations
Marvel
⭐
7
Multigranular Analysis of Regulatory Variants on the Epigenomic Landscape
Rbcf
⭐
7
R Bindings for htslib/bcf
Annotatemaf
⭐
7
Add functional variant annotation to MAF file
Bamsplit
⭐
7
Split a BAM file by haplotype support
Malva
⭐
7
genotyping by Mapping-free ALternate-allele detection of known VAriants
Tersect
⭐
6
Command-line utility for conducting fast set theoretical operations and genetic distance estimation on biological sequence variant data.
Kf Jointgenotyping Workflow
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6
🔬 Joint genotyping workflow for Kids-First DRC
Clinvar Kaggle
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6
Scripts related to the ClinVar conflicting classifications dataset on Kaggle
Renovo
⭐
6
Clinical machine-learning based interpreter of germline mutations.
Lamprey
⭐
6
A Loop-Mediated Isothermal Amplification (LAMP) concatemer analysis, variant calling, and polishing tool
Bioapi Examples
⭐
6
Code examples for working with web based bioinformatics APIs
Covseq
⭐
6
CoV-Seq: COVID-19 Genomic Sequence Database and Visualization
Bionode Example Dat Gasket
⭐
5
Bionode Example with Dat and Gasket
Varity
⭐
5
Variant translation library for Clojure
Mutationinfo
⭐
5
Tool to retrieve location information of genetic variants
Gnomic
⭐
5
A grammar for describing microbial genotypes and phenotypes
Eva
⭐
5
Efficient Variant Analysis
Vase
⭐
5
Variant Annotation, Segregation and Exclusion for family or cohort based rare-disease sequencing studies.
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