Human Genetics Informatics (HGI)

Human Genetics

We help the Human Genetics faculty groups evaluate and access the best methods to process and absorb the huge amounts of sequencing data produced by modern studies at Sanger. In practice, this means creating, testing and running variant-calling pipelines, RNASeq pipelines and annotation pipelines on cohorts of tens of thousands of genomes, exomes and transcriptomes.

All this requires superb understanding and control of:

The Sanger’s High Performance Compute architecture (many server farms with thousands of cores)
The Sanger’s OpenStack Flexible Compute Architecture and how to reliably deploy into it
Frameworks to run biological pipelines (e.g. Cromwell, NextFlow)
Frameworks to store, annotate, filter and analyse very large amounts of genomic variant data (e.g. Hail , or more experimental software such as Tachyon)
Tools to help us view and account for our storage and processing

We rely on Sanger’s systems teams, and cooperate extensively with Sanger core teams and other Sanger program informatics teams such as Cancer Informatics and Cell Gen Informatics to share experience and practice.

We aim to deliver data in a reliable way and continously improve how and what we deliver. One thing is clear – we can no longer hand over vcf files and call it a day! Interested? Come talk to us!

Our people

Group lead

Vivek Iyer

Human Genetics Informatics Team Lead

Core team

Mr Sendu Bala

Principle Software Developer

Allan Daly

Senior Bioinformatician

Dr Ruth Eberhardt

Senior Bioinformatician

Dr Matiss Ozols

Principal Bioinformatician

Dr Mark Thomas

Principal Bioinformatician

Previous core team members

Piyush Ahuja

Senior Software Developer

Dr Pavlos Antoniou

Principal Software Developer

Irina Gabriela Colgiu

Senior Software Developer

Dr Edgar Garriga Nogales

Senior Bioinformatician

Christopher Harrison

Senior Software Developer

Emyr James

Principal Systems Administrator / Principal DevOps Engineer

Filip Makosza

Sandwich Year Placement

Dr Guillaume Noell

Senior Software Developer

Colin Nolan

Former Group Leader (Acting)

Dr Hannes Ponstingl

Principal Bioinformatician

Dr Joshua C. Randall

Senior Scientific Manager

Associated research

Tools & software

Tool

Hail analysis pipelines

Hail based analysis pipelines for HG projects: pipelines for QC of genome - sequenced cohorts, and GWAS after QC. Designed to ...

Tool

Hgi Cloud

Terraform and ansible codebase to provision clusters (e.g. hail/spark) at Sanger. The framework can be used to provision ...

Tool

Nextflow-RNASeq

A bioinformatics analysis pipeline used for RNA sequencing data, written in the new nextflow DSL2 language syntax, leveraging nextflow modules.

Tool

Shepherd

This code performs targeted archiving of the files arising from the analysis of Sanger sequencing projects.

Tool

Weaver

Browser-based Shiny frontend to view internal Lustre volume reports.

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