Sequence Analysis and Management (SAM) | Scientific Operations

Sequence Analysis and Management (SAM) | Scientific Operations

Sequence Analysis and Management (SAM)

sam-infomatics-3.jpgSanger Institute, Genome Research Limited

Our Research and Approach

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.

People

Davies, Robert
Robert Davies
Group Leader

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.

Key Projects, Collaborations, Tools & Data

Partners and Funders

Internal Partners

Publications

  • Comparison of high-throughput sequencing data compression tools.

    Numanagić I, Bonfield JK, Hach F, Voges J, Ostermann J et al.

    Nature methods 2016;13;12;1005-1008

  • Gap5--editing the billion fragment sequence assembly.

    Bonfield JK and Whitwham A

    Bioinformatics (Oxford, England) 2010;26;14;1699-703

  • Genome-wide end-sequenced BAC resources for the NOD/MrkTac() and NOD/ShiLtJ() mouse genomes.

    Steward CA, Humphray S, Plumb B, Jones MC, Quail MA et al.

    Genomics 2010;95;2;105-10

  • Improvements to services at the European Nucleotide Archive.

    Leinonen R, Akhtar R, Birney E, Bonfield J, Bower L et al.

    Nucleic acids research 2010;38;Database issue;D39-45

  • Petabyte-scale innovations at the European Nucleotide Archive.

    Cochrane G, Akhtar R, Bonfield J, Bower L, Demiralp F et al.

    Nucleic acids research 2009;37;Database issue;D19-25

  • Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database.

    Cochrane G, Akhtar R, Aldebert P, Althorpe N, Baldwin A et al.

    Nucleic acids research 2008;36;Database issue;D5-12

  • A genome-wide, end-sequenced 129Sv BAC library resource for targeting vector construction.

    Adams DJ, Quail MA, Cox T, van der Weyden L, Gorick BD et al.

    Genomics 2005;86;6;753-8

  • Shotgun haplotyping: a novel method for surveying allelic sequence variation.

    Lindsay SJ, Bonfield JK and Hurles ME

    Nucleic acids research 2005;33;18;e152

  • The genome of the African trypanosome Trypanosoma brucei.

    Berriman M, Ghedin E, Hertz-Fowler C, Blandin G, Renauld H et al.

    Science (New York, N.Y.) 2005;309;5733;416-22

  • The genome of the kinetoplastid parasite, Leishmania major.

    Ivens AC, Peacock CS, Worthey EA, Murphy L, Aggarwal G et al.

    Science (New York, N.Y.) 2005;309;5733;436-42

  • Complex haplotypes, copy number polymorphisms and coding variation in two recently divergent mouse strains.

    Adams DJ, Dermitzakis ET, Cox T, Smith J, Davies R et al.

    Nature genetics 2005;37;5;532-6

  • Mutagenic insertion and chromosome engineering resource (MICER).

    Adams DJ, Biggs PJ, Cox T, Davies R, van der Weyden L et al.

    Nature genetics 2004;36;8;867-71

  • The DNA sequence of chromosome I of an African trypanosome: gene content, chromosome organisation, recombination and polymorphism.

    Hall N, Berriman M, Lennard NJ, Harris BR, Hertz-Fowler C et al.

    Nucleic acids research 2003;31;16;4864-73

  • Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13.

    Hall N, Pain A, Berriman M, Churcher C, Harris B et al.

    Nature 2002;419;6906;527-31

  • Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18.

    Parkhill J, Dougan G, James KD, Thomson NR, Pickard D et al.

    Nature 2001;413;6858;848-52

  • Genome sequence of Yersinia pestis, the causative agent of plague.

    Parkhill J, Wren BW, Thomson NR, Titball RW, Holden MT et al.

    Nature 2001;413;6855;523-7

  • An SNP map of human chromosome 22.

    Mullikin JC, Hunt SE, Cole CG, Mortimore BJ, Rice CM et al.

    Nature 2000;407;6803;516-20

  • Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491.

    Parkhill J, Achtman M, James KD, Bentley SD, Churcher C et al.

    Nature 2000;404;6777;502-6

  • The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences.

    Parkhill J, Wren BW, Mungall K, Ketley JM, Churcher C et al.

    Nature 2000;403;6770;665-8

  • The complete nucleotide sequence of chromosome 3 of Plasmodium falciparum.

    Bowman S, Lawson D, Basham D, Brown D, Chillingworth T et al.

    Nature 1999;400;6744;532-8

  • Automated detection of point mutations using fluorescent sequence trace subtraction.

    Bonfield JK, Rada C and Staden R

    Nucleic acids research 1998;26;14;3404-9

  • Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence.

    Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C et al.

    Nature 1998;393;6685;537-44