Wellcome Sanger Institute

High Performance Algorithm Group (HPAG)

Science Solutions - Informatics and Digital Solutions

Many high profile projects such as the Cancer Genome and 1000 Genomes projects need quality assemblies for downstream analysis using 2nd and 3rd generation sequencing data. Efficient bioinformatics tools in processing and analysis of large quantities of genomic data play crucial roles in producing high quality assemblies as well as variation detection. The High Performance Algorithm Group (HPAG), headed by Zemin Ning, develops algorithms and software tools for genome analysis. Currently the team is also involved in data processing and quality evaluation of Oxford Nanopore sequencing technology.

Development of genome assembly tools using second and third generation sequencing data
Efficient algorithms for detecting structural variations from single molecule sequencing data
Detection of segmental duplications from kmer distribution profiles

Our people

Group lead

Dr Zemin Ning

Senior Scientific Manager

Zemin oversees the activities of the group. He interacts with both internal and external collaborators on various projects, while providing technical guidance and support for the group members. He is also actively involved in algorithm development and code programming.

Previous team members

Dr Francesca Giordano

Postdoctoral Fellow

Associated research

Tools & software

Tool

Cross_genome

An efficient scaffoding tool using cross genome species synteny.

Tool

Phusion

Phusion: A read clustering based assembly algorithm using capillary sequencing data.

Tool

Phusion2

Phusion2 is a pipeline for de novo genome assembly using NGS data.

Tool

Pindel

An effective tool, based on the Pattern Growth algorithm to detect breakpoints of large indels.

Tool

SMALT

SMALT efficiently aligns DNA sequencing reads with a reference genome.Reads from a wide range of sequencing platforms, for example Illumina, ...

Tool

SMIS

SMIS ( Single Molecular Integrative Scaffolding ): an assembly pipeline to improve genome scaffolding using Oxford Nanopore or PacBio long reads.

Tool

SSAHA

SSAHA ( Sequence Search and Alignment by Hashing Algorithm ) is a software tool for very fast matching and alignment of DNA sequences.

Tool

SSAHA2

SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) is a pairwise sequence alignment program designed for the efficient mapping of sequencing ...

Related groups

Science group

DNA Pipelines Research and Development

DNA Pipelines Development

The DNA Pipelines Research and Development group is the entry point for new technologies to the Institute, especially sequencing instruments. The ...

Science group

Genome Reference Informatics Team

Tree of Life Programme

Collaborate on the generation of zebrafish assemblies.

Science group

New Pipeline Group (NPG)

Sequencing Informatics

HPA has created tools which are essential components of NPG's current analysis pipelines and leads on developing and testing software ...

Science group

Sequence Analysis and Management (SAM)

Science Support - Informatics and Digital Solutions

The Sequence Analysis and Management team contributes to various software packages for processing DNA sequence data, including samtools, htslib, biobambam and ...

Wellcome Sanger Institute

Programmes and Facilities

Programme

Science Solutions

Science Solutions directly partners with the Sanger Institute’s scientists at all levels to anticipate and supply their data science related ...

Programme

Informatics and Digital Solutions

We support the Sanger Institute’s mission to deliver innovative and ambitious genomics research at a scale to improve human health ...

Partners

We work with the following groups

External

Transmissible Cancer

Work with Dr Elizabeth Murchison on Tasminan Devil pan-cancer genome project.

Publications

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