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

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

PEPPER-Margin-DeepVariant

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.

[THIS REPO IS DEPRECATED] see newer repos: https://github.com/broadinstitute/viral-core https://github.com/broadinstitute/viral-assemble https://github.com/broadinstitute/viral-phylo https://github.com/broadinstitute/viral-classify https://github.com/broadinstitute/viral-pipelines

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

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.

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.

Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling

ClairS-TO - a deep-learning method for tumor-only somatic variant calling

A tool for fast and accurate summarizing of variant calling format (VCF) files

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

Deep Learning based variant calling toolkit - https://clara-parabricks.github.io/VariantWorks/

Reference-free variant discovery in large eukaryotic genomes

Clair3-RNA - a long-read small variant caller for RNA sequencing data

Complex structural variant detection from WGS data

Use an ensemble of variant callers to call variants from ATAC-seq data

Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting.

Evaluating Nanopore-based bacterial variant calling

rMETL - realignment-based Mobile Element insertion detection Tool for Long read