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Search results for genomics vcf
genomics
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vcf
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65 search results found
Vg
⭐
1,022
tools for working with genome variation graphs
Hail
⭐
905
Cloud-native genomic dataframes and batch computing
Nucleus
⭐
675
Python and C++ code for reading and writing genomics data.
Snippy
⭐
408
✂️ ⚡ Rapid haploid variant calling and core genome alignment
Cyvcf2
⭐
345
cython + htslib == fast VCF and BCF processing
Vcfanno
⭐
334
annotate a VCF with other VCFs/BEDs/tabixed files
Truvari
⭐
284
Structural variant toolkit for VCFs
Hap.py
⭐
283
Haplotype VCF comparison tools
Htsjdk
⭐
271
A Java API for high-throughput sequencing data (HTS) formats.
Rtg Tools
⭐
260
RTG Tools: Utilities for accurate VCF comparison and manipulation
Pygeno
⭐
242
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Vcfr
⭐
225
Tools to work with variant call format files
Somalier
⭐
224
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
Kipoi
⭐
222
Kipoi's model zoo API
Slivar
⭐
221
genetic variant expressions, annotation, and filtering for great good.
Smoove
⭐
173
structural variant calling and genotyping with existing tools, but, smoothly.
Genomics
⭐
154
A collection of scripts and notes related to genomics and bioinformatics
Genozip
⭐
144
A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too
Jigv
⭐
115
igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"
Peddy
⭐
104
genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF
Cljam
⭐
87
A DNA Sequence Alignment/Map (SAM) library for Clojure
Tiledb Vcf
⭐
79
Efficient variant-call data storage and retrieval library using the TileDB storage library.
Svtyper
⭐
78
Bayesian genotyper for structural variants
Bgt
⭐
76
Flexible genotype query among 30,000+ samples whole-genome
Duphold
⭐
73
don't get DUP'ed or DEL'ed by your putative SVs.
Scoary
⭐
71
Pan-genome wide association studies
Simug
⭐
58
simuG: a general-purpose genome simulator
Vcfdist
⭐
48
vcfdist: Accurately benchmarking phased variant calls
Hts Nim Tools
⭐
41
useful command-line tools written to show-case hts-nim
Indelope
⭐
39
find large indels (in the blind spot between GATK/freebayes and SV callers)
Gor
⭐
37
GORpipe is a tool based on a genomic ordered relational architecture and allows analysis of large sets of genomic and phenotypic tabular data using declarative query language, in a parallel execution engine.
Disq
⭐
31
A library for manipulating bioinformatics sequencing formats in Apache Spark
Varsome Api Client Python
⭐
26
Example client programs for Saphetor's VarSome annotation API
Cerebra
⭐
26
A tool for fast and accurate summarizing of variant calling format (VCF) files
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
Sv Pipeline
⭐
21
Pipeline for structural variation detection in cohorts
Iliad
⭐
21
ILIAD: A suite of automated Snakemake workflows for processing genomic data for downstream applications
Cmdbtools
⭐
21
Command line tools for CMDB varaints browser
Vcf2fhir
⭐
20
vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration
Variant_catalogue_pipeline
⭐
20
Variant catalogue pipeline
Ontologies
⭐
16
Home of the Genomic Feature and Variation Ontology (GFVO)
Spark Vcf
⭐
15
Spark VCF data source implementation for Dataframes
Variantdb_challenge
⭐
14
Finding a scalable alternative to the VCF File for genomics analysis
Tiledb Examples
⭐
13
Notebooks which are dedicated examples for TileDB
Misc Genomics Tools
⭐
13
assorted scripts for doing genomics
Vsnp
⭐
13
vSNP -- validate SNPs
Mitty
⭐
13
Seven Bridges Genomics aligner/caller debugging and analysis tools
Rsidx
⭐
12
Library for indexing VCF files for random access searches by rsID
Divbrowse
⭐
10
A web application for interactive visualization and exploratory data analysis of variant call matrices
Ucscbeacon
⭐
10
A GA4GH Draft Beacon implementation
Vcfpp
⭐
9
a C++ API of htslib to be easily integrated and safely used. More importantly, it can be callled seamlessly in R/Python/Julia etc.
Bamscope
⭐
7
A command line tool (in Kotlin/JVM) for intuitively visualizing BAM alignments.
Popgen
⭐
7
Small scripts for population genetics analysis
Agaat
⭐
7
Automated Tool for Global Screening Array analysis
Genotype
⭐
7
Simple genotype comparison of VCF files
Ipat
⭐
7
iPat allows you to perform GWAS and GS with drags and clicks!
Xvcf Rs
⭐
6
VCF/BCF [un]compressed [un]indexed
Tersect
⭐
6
Command-line utility for conducting fast set theoretical operations and genetic distance estimation on biological sequence variant data.
Unmasc
⭐
6
Tumor-only variant calling
Broad Fungalgroup
⭐
6
Broad Fungal Genomics group scripts
Recallme
⭐
5
Repository for RecallME-v.0.1 a variant calling pipelines benchmarker and optimizer
Bpbio
⭐
5
basepair bio: a single binary with many useful genomics subtools.
Vcfwrenchr
⭐
5
Basic R package for VCF reformatting (json and tab-delimited text)
Spark Gatk
⭐
5
Spark-GATK is a genomics analysis framwork based on Apache Spark and ADAM.
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1-65 of 65 search results
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