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

✂️ ⚡ Rapid haploid variant calling and core genome alignment

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

Bayesian haplotype-based mutation calling

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

PEPPER-Margin-DeepVariant

Fast and accurate gene fusion detection from RNA-Seq 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.

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

Viral genomics analysis pipelines

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

Graph realignment tools for structural variants

Sequana: a set of Snakemake NGS pipelines

Long read production pipelines

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

GATK RNA-Seq Variant Calling in Nextflow

A lightweight and 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.

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

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