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Search results for c plus plus vcf

76 search results found

tools for working with genome variation graphs

Nucleus ⭐ 675

Python and C++ code for reading and writing genomics data.

Nanopolish ⭐ 496

Signal-level algorithms for MinION data

Vcftools ⭐ 415

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

Survivor ⭐ 299

Toolset for SV simulation, comparison and filtering

Haplotype VCF comparison tools

Structural variation and indel detection by local assembly

Poplddecay ⭐ 138

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files

SMC++ infers population history from whole-genome sequence data.

Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species

Genome browser and variant annotation

Pan-genome inference and genotyping with long noisy or short accurate reads

Tiledb Vcf ⭐ 79

Efficient variant-call data storage and retrieval library using the TileDB storage library.

Sparse Project VCF: evolution of VCF to encode population genotype matrices efficiently

Minimac4 ⭐ 50

vcfdist: Accurately benchmarking phased variant calls

a string to graph aligner

Population-wide Deletion Calling

Ngsrelate ⭐ 31

Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact (Illumina) reads.

Efficient program for calculating Extended Haplotype Homozygosity (EHH) and Integrated Haplotype Score (iHS)

Leviosam ⭐ 27

Lift-over alignments from variant-aware references

Mergesvcallers ⭐ 26

heuristics to merge structural variant calls in VCF format.

Graphite ⭐ 25

Graphite - Graph-based variant adjudication

Minimac3 ⭐ 24

Minimac3 is a low memory and computationally efficient implementation of the genotype imputation algorithms. Minimac3 is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy.

simple viewer for variant call format using htslib

Gvcfgenotyper ⭐ 23

A utility for merging and genotyping Illumina-style GVCFs.

Glactools ⭐ 23

command-line tools for the management of genotype likelihoods and allele counts

scSNV Mapping tool for 10X Single Cell Data

A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools

Repeatseq ⭐ 19

Accurate microsatellite genotypes from high-throughput resequencing data

Fast Structural Variation Detection Toolbox

haplotypes genotypes and alleles example decision synthesizer

Svcollector ⭐ 17

Method to optimally select samples for validation and resequencing

Towards fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.

Anno is a variant annotation tool

UVC, a very accurate small-variant caller (https://doi.org/10.1093/bib/bbab458)

Eurorack ⭐ 14

Eurorack Module Designs, often based on popular designs but modified to be even more...escalative.

Read_haps ⭐ 13

Detects human contamination in bam files

Vcv_nozori ⭐ 13

port of nozori eurorack module for VCV Rack

GenoTypes Compressor

Strdenovotools ⭐ 11

Toolkit for calling and analyzing de novo STR mutations

Vbt Trioanalysis ⭐ 10

Cloudict ⭐ 10

A game engine for Connect6, using min-max search, alpha-beta prunning, and VCF search.

Minisynth ⭐ 9

A Simple VST Synthesizer

a C++ API of htslib to be easily integrated and safely used. More importantly, it can be callled seamlessly in R/Python/Julia etc.

Gap2Seq is a gap filling and insertion genotyping tool.

Rrselection ⭐ 9

RRSelection: A linkage disequilibrium method to detect selection region across population VCF

Pg Instruments ⭐ 8

VCV PG Instruments

robust matching of small variant datasets using flexible scoring schemes

Biocpp Io ⭐ 8

BioC++ Input/Output library

Scidb Genotypes ⭐ 7

Adds support to SciDB for loading genotype data from VCF files.

Ngs_server ⭐ 7

Ultra Lightweight NGS (BAM/VCF) Server

Snowmansv ⭐ 7

Structural variation and indel detection using rolling local string graph assembly

A tool for phasing and imputing haplotypes in 10k+ low coverage sequencing samples

Arduino_monotron ⭐ 6

Code for Arduino to control a Korg Monotron via MIDI

Sgx Genome Variants Search ⭐ 6

🔨 Tool for GWAS summary-level data analysis

annotation of variants using genotype likelihoods

Convert Variant Call Format (VCF) file to genotype file

Novocaller ⭐ 6

Heuristic, parsimony-based ancestral recombination graph inference

Dosageconvertor ⭐ 6

DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3/4 to other formats such as MaCH or PLINK.

Metalnx Msi ⭐ 5

Metalnx Micro Services for iRODS

Robust Unified Hardy-Weinberg Equilibrium Test

Cleancall ⭐ 5

Correction for DNA contamination in genotype calling

fasta files from vcf file(s)

Convert structural variants to sequence graphs [ VCF + FASTA ---> GFA ]

Artic Tools ⭐ 5

a set of tools for viral amplicon schemes

Allele frequency counter with BAM file and VCF file

Submission to iDASH competition 2016 task3

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