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Search results for sequencing vcf

30 search results found

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

Truvari ⭐ 284

Structural variant toolkit for VCFs

A Java API for high-throughput sequencing data (HTS) formats.

Genomics ⭐ 154

A collection of scripts and notes related to genomics and bioinformatics

Ngscheckmate ⭐ 106

Software program for checking sample matching for NGS data

Parliament2 ⭐ 83

Runs a combination of tools to generate structural variant calls on whole-genome sequencing data

Neat Genreads ⭐ 72

NEAT read simulation tools

Opengene.jl ⭐ 61

(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia

Sv Plaudit ⭐ 47

Pipeline for structural variant image curation and analysis.

Snpsplit ⭐ 43

Allele-specific alignment sorting

Platinumgenomes ⭐ 42

The Platinum Genomes Truthset

Seqminer ⭐ 28

Query sequence data (VCF/BCF1/BCF2, Tabix, BGEN, PLINK) in R

QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.

Variant Filter ⭐ 25

A false-positive filter for variants called from massively parallel sequencing

Tool to find regions of homozygosity (ROHs) from sequencing data.

Helmsman ⭐ 19

highly-efficient & lightweight mutation signature matrix aggregation

Code for multi-sample variant calling from sequence data of pooled or unpooled DNA samples

180+ Java applications for analyzing next generation sequencing data from ChIPSeq, RNASeq, BisSeq, DNASeq, variant annotation/ filtering, alignment/VCF QC, capture array design, IGV/ DAS2/IGB/UCSC file manipulation, etc. Both GUI and cmd line interfaces.

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

Parsecnv2 ⭐ 14

Parse Copy Number Variation from Array and Sequencing

Groovy Ngs Utils ⭐ 12

A collection of utilities for working with next generation (MPS) sequencing data in Groovy

Horizontal Gene Transfer Detection by Mapping Sequencing Reads

Hadoopcnv ⭐ 12

HadoopCNV is a MapReduce-based copy number variation caller for genome sequencing data

Cau Tibetanwheatseq ⭐ 10

Customized codes used in Tibetan wheat sequencing project.

Seq Collection ⭐ 9

Simulate next-generation sequencing reads for tumor samples

Scnaphase ⭐ 8

Profile haploid somatic copy number alterations,especially for NGS sequencing data on significantly contaminated tumor samples

Combine structural variation outputs from long sequencing reads into a superior call set

Nf Gatk_exome_preprocess ⭐ 6

Adapted from the GATK best practice guide to preprocess whole exome sequencing (WES) data

Haplocheck ⭐ 6

Phylogeny-based Contamination Detection in Mitochondrial and Whole-Genome Sequencing Studies

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