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Search results for variant calling
variant-calling
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86 search results found
Jcvi
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650
Python library to facilitate genome assembly, annotation, and comparative genomics
Vcflib
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594
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
Snippy
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408
✂️ ⚡ Rapid haploid variant calling and core genome alignment
Sarek
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299
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Octopus
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285
Bayesian haplotype-based mutation calling
Pepper
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216
PEPPER-Margin-DeepVariant
Clair3
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191
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
Megalodon
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172
Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.
Arriba
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165
Fast and accurate gene fusion detection from RNA-Seq data
Vt
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163
A tool set for short variant discovery in genetic sequence data.
Clairvoyante
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142
Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
Paragraph
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140
Graph realignment tools for structural variants
Sequana
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136
Sequana: a set of Snakemake NGS pipelines
Viral Ngs
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129
Viral genomics analysis pipelines
Long Read Pipelines
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108
Long read production pipelines
Viralrecon
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101
Assembly and intrahost/low-frequency variant calling for viral samples
Tracy
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92
Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files
Fermikit
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91
De novo assembly based variant calling pipeline for Illumina short reads
Gramtools
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90
Genome inference from a population reference graph
Ilus
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89
A handy variant calling pipeline generator for whole-genome sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.
Genomicsdb
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88
High performance data storage for importing, querying and transforming variants.
Mccortex
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86
De novo genome assembly and multisample variant calling
Nullarbor
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80
💾 📃 "Reads to report" for public health and clinical microbiology
Tiledb Vcf
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79
Efficient variant-call data storage and retrieval library using the TileDB storage library.
Callings Nf
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76
GATK RNA-Seq Variant Calling in Nextflow
Dysgu
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75
Toolkit for calling structural variants using short or long reads
Grenepipe
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75
A flexible, scalable, and reproducible pipeline to automate variant calling from sequence reads.
Clair
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74
Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling
Raredisease
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64
Call and score variants from WGS/WES of rare disease patients.
Hla
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57
xHLA: Fast and accurate HLA typing from short read sequence data
Ivar
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53
iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
Bayestyper
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52
A method for variant graph genotyping based on exact alignment of k-mers
Vcfdist
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48
vcfdist: Accurately benchmarking phased variant calls
Kevlar
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42
Reference-free variant discovery in large eukaryotic genomes
Balsamic
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40
Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
Ococo
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39
Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.
Indelope
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39
find large indels (in the blind spot between GATK/freebayes and SV callers)
Variantworks
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38
Deep Learning based variant calling toolkit - https://clara-parabricks.github.io/VariantWorks/
Deepvariant
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38
Google's DeepVariant variant caller as a Nextflow pipeline
Chm Eval
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37
Popdel
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32
Population-wide Deletion Calling
Indigo
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29
Indigo: SNV and InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products
Cerebra
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26
A tool for fast and accurate summarizing of variant calling format (VCF) files
Rnavar
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23
gatk4 RNA variant calling pipeline
Germline Dna
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23
A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample
Ngs Variants Training
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22
GitHub for the SIB courses NGS - Genome variant analysis
Varca
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20
Use an ensemble of variant callers to call variants from ATAC-seq data
Uncovar
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19
Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting.
Arcsv
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19
Complex structural variant detection from WGS data
Gatk4_best_practice
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18
GATK4 Best Practice Nextflow Pipeline
Clairs To
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18
ClairS-TO - a deep-learning method for tumor-only somatic SNV calling
Rna Seq Pop
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17
Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data
Rmetl
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16
rMETL - realignment-based Mobile Element insertion detection Tool for Long read
Sentieon Dnaseq
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15
Sentieon DNAseq
Clair3 Trio
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12
Clair3-Trio: variant calling in trio using Nanopore long-reads
Workshop Ngsintro
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12
Workshop • Intro to Bioinformatics using NGS data • 5 days
Microphaser
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11
Genome On Diet
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11
Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metagenomic profiling. It is much faster & more memory-efficient than minimap2 for Illumina, HiFi, and ONT reads. Described by Alser et al. (preliminary version: https://arxiv.org/abs/2211.08157).
Vipr
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10
Assembly and intrahost / low-frequency variant calling for viral samples
Npore
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10
nPoRe: n-Polymer Realigner for improved pileup-based variant calling
Bioinformatics
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10
A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common DNA and RNA sequence analysis methods.
Exoseq
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10
Please consider using/contributing to https://github.com/nf-core/sarek
Tbpore
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9
Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
Dv Trio
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8
dv-trio provides a pipeline to call variants for a trio (father-mother-child) using DeepVariants [1]. Genomic Variant Calling Files (gVCFs) created by DeepVariants are then co_called together using GATK[2]. The resultant trio VCF is then post-processing with FamSeq[3] to eliminate mendelian errors.
Nrex
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8
nRex: Germline and somatic single-nucleotide, short indel and structural variant calling
Strainflye
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7
Pipeline for analyzing (rare) mutations in metagenome-assembled genomes
Somatic Variantcalling
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7
A pipeline for somatic variantcalling. Category:Single-Sample
Imputation_beagle_tutorial
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7
Imputation-beagle-tutorial
Varathon
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7
A scalable variant calling and benchmarking framework supporting both short and long reads.
Snvcallingworkflow
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7
The DKFZ-ODCF, formerly DKFZ/eilslabs SNV-Calling Workflow
Sentieon Dnascope Ml
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7
Sentieon DNAscope + Machine Learning Model
Mgp1000
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7
Nextflow bioinformatics pipeline for large-scale analysis of Multiple Myeloma genomes
Snipgenie
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6
command line and desktop tool for microbial variant calling
Corticall
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6
Germline DNM caller based on LdBG assembly of pathogens
Novocaller
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6
Rmahunter
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6
Harpy
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6
Process raw haplotagging data, from raw sequences to phased haplotypes, batteries included.
Sequencevariation.jl
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6
Biological sequence variation
Reads2map
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6
WDL workflows to build genetic maps from sequencing reads
Nf Ncov Voc
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5
A Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 genomes (Variants of Concern and Variants of Interest). Workflow is developed in collaboration with COVID-MVP (https://github.com/cidgoh/COVID-MVP) which can be used to visualize the mutation profiles and functional annotations.
Allmine
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5
AllMine, a flexible pipeline for Allele Mining. Develloped at INRA's GAFL unit :
Variant Calling At Scale
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5
Scalable and High Performance Variant Calling on Cluster Environments
Rdxon
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5
Reference-free FASTQ filter for rare germline and somatic variants
Clair3 Rna
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5
Clair3-RNA - long-read short variant caller for RNA sequencing data
Lofreq Fpga
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5
FPGA Acceleration for the LoFreq variant caller
Nextflow_varcal
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5
Nextflow Tutorial - Variant Calling Edition
Related Searches
Bioinformatics Variant Calling (48)
Python Variant Calling (47)
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