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

:scissors: :zap: 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

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

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-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

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology

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.

GATK RNA-Seq Variant Calling in Nextflow

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files

Toolkit for calling structural variants using short or long reads

Call and score variants from WGS/WES of rare disease patients.

xHLA: Fast and accurate HLA typing from short read sequence data

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.

De novo genome assembly and multisample variant calling

De novo assembly based variant calling pipeline for Illumina short reads

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

Efficient variant-call data storage and retrieval library using the TileDB storage library.

High performance data storage for importing, querying and transforming variants.