variant-calling

Python library to facilitate genome assembly, annotation, and comparative genomics

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

✂️ ⚡ Rapid haploid variant calling and core genome alignment

Clair3 - Symphonizing pileup and full-alignment for deep learning-based long-read variant calling

Bayesian haplotype-based mutation calling

Fast and accurate gene fusion detection from RNA-Seq data

PEPPER-Margin-DeepVariant

A tool set for short variant discovery in genetic sequence data.

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.

viral-ngs: command line tools and wrappers for processing raw viral genomic data

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

Graph realignment tools for structural variants

Assembly and intrahost/low-frequency variant calling for viral samples

Long read production pipelines

Sequana: a set of Snakemake NGS pipelines

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.

💾 📃 "Reads to report" for public health and clinical microbiology

GATK RNA-Seq Variant Calling in Nextflow

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.