variant-calling
There are 291 repositories under variant-calling topic.
tanghaibao/jcvi
Python library to facilitate genome assembly, annotation, and comparative genomics
vcflib/vcflib
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
tseemann/snippy
:scissors: :zap: Rapid haploid variant calling and core genome alignment
nf-core/sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
luntergroup/octopus
Bayesian haplotype-based mutation calling
HKU-BAL/Clair3
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
kishwarshafin/pepper
PEPPER-Margin-DeepVariant
suhrig/arriba
Fast and accurate gene fusion detection from RNA-Seq data
nanoporetech/megalodon
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.
atks/vt
A tool set for short variant discovery in genetic sequence data.
broadinstitute/viral-ngs
Viral genomics analysis pipelines
aquaskyline/Clairvoyante
Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
Illumina/paragraph
Graph realignment tools for structural variants
broadinstitute/long-read-pipelines
Long read production pipelines
sequana/sequana
Sequana: a set of Snakemake NGS pipelines
nf-core/viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples
ShujiaHuang/ilus
A lightweight and handy variant calling pipeline generator for whole-genome sequencing (WGS) and whole exom sequencing data (WES) analysis by using GATK and Sentieon. 一个基于 GATK 和 Sentieon 的简易且全面的 WGS/WES 分析流程生成器.
tseemann/nullarbor
:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
CRG-CNAG/CalliNGS-NF
GATK RNA-Seq Variant Calling in Nextflow
andersen-lab/ivar
iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
PacificBiosciences/ccs
CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)
gear-genomics/tracy
Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files
humanlongevity/HLA
xHLA: Fast and accurate HLA typing from short read sequence data
mcveanlab/mccortex
De novo genome assembly and multisample variant calling
kcleal/dysgu
Toolkit for calling structural variants using short or long reads
nf-core/raredisease
Call and score variants from WGS/WES of rare disease patients.
lh3/fermikit
De novo assembly based variant calling pipeline for Illumina short reads
moiexpositoalonsolab/grenepipe
A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles - for sampled individuals, and for pool sequencing.
HKU-BAL/Clair
Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling
GenomicsDB/GenomicsDB
High performance data storage for importing, querying and transforming variants.
TileDB-Inc/TileDB-VCF
Efficient variant-call data storage and retrieval library using the TileDB storage library.
iqbal-lab-org/gramtools
Genome inference from a population reference graph
lh3/minipileup
Simple pileup-based variant caller
bioinformatics-centre/BayesTyper
A method for variant graph genotyping based on exact alignment of k-mers
TimD1/vcfdist
vcfdist: Accurately benchmarking phased variant calls
czbiohub-sf/cerebra
A tool for fast and accurate summarizing of variant calling format (VCF) files