Wellcome Sanger Institute

Sequence Analysis and Management (SAM)

Sequencing Informatics

SAM contributes to various software packages for processing DNA sequence data, including samtools, htslib, biobambam and the Staden package.

We also submit raw sequencing data to the EBI on behalf of the research groups.

Our people

Group lead

Robert Davies

Senior Scientific Manager

Robert joined the Sanger Centre (as it was then) in 1994. Since then he has worked on robotics, Pathogen assemblies, a variety of database systems, archiving tools and sequence processing pipelines.

Core team

James Bonfield

Principal Software Developer

Andrew Whitwham

Senior Software Developer

Associated research

Tools & software

Tool

CRAM

CRAM is a more highly compressed alternative to the BAM and SAM DNA sequence alignment file formats.

Tool

Crumble

Crumble - Lossy compression of DNA sequence quality values

Tool

Gap5

Gap5 is a DNA sequence assembly visualiser and editing tool.

Tool

SAMtools / BCFtools / HTSlib

SAMtools, BCFtools. and HTSlib are tools for manipulating sequence alignment (SAM, BAM, CRAM) and variant call (VCF and BCF) files.

Tool

Scramble

Scramble is a DNA sequencing file format conversion tool included as part of the Staden io_lib package.

Tool

teepot

teepot is a buffered version of the unix tee command.

Related groups

Science group

High Performance Algorithm Group (HPAG)

Sequencing Informatics

Many high profile projects such as the Cancer Genome and 1000 Genomes projects need quality assemblies for downstream analysis using 2nd ...

Science group

New Pipeline Group (NPG)

Sequencing Informatics

The SAM team is responsible for archival of the data produced by NPG to external repositories, typically the EGA, ENA or ...

Science group

Production Software Development

Laboratory Information and Management Systems (LIMS) compute and infrastructure

We create and support the software and systems the Sanger Institute’s scientists rely at every step of their experiments. We ...

Science group

Sequence Variation Infrastructure

Human Genetics

Collaborate on development of Samtools and maintenance of the sequencing data format specifications (SAM/BAM/CRAM/BCF/VCF).

Science group

Vertebrate Resequencing

Informatics

The Vertebrate Resequencing (VR) team was responsible for handling the informatics and large scale sequencing projects for the Durbin and Adams ...

Wellcome Sanger Institute

Programmes and Facilities

Programme

Information Communications Technology

Our goal is "To provide World Class High Performance Computing and First Class Production Platforms and Services for genome and biodata ...

Partners

We work with the following groups

External

European Bioinformatics Institute

External

National Center for Biotechnology Information (NCBI)

Publications

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