Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
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Updated
Jun 4, 2024 - Nextflow
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
Python library to facilitate genome assembly, annotation, and comparative genomics
✂️ ⚡ Rapid haploid variant calling and core genome alignment
Assembly and intrahost/low-frequency variant calling for viral samples
Viral genomics analysis pipelines
GATK RNA-Seq Variant Calling in Nextflow
xHLA: Fast and accurate HLA typing from short read sequence data
Fast and accurate gene fusion detection from RNA-Seq data
Variant Calling Pipeline Using GATK4 and Nextflow
PEPPER-Margin-DeepVariant
iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
Bayesian haplotype-based mutation calling
💾 📃 "Reads to report" for public health and clinical microbiology
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.
Call and score variants from WGS/WES of rare disease patients.
CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)
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.
GATK4 Best Practice Nextflow Pipeline
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