Imperial College London

ProfessorMichaelSternberg

Faculty of Natural SciencesDepartment of Life Sciences

Director Centre for Bioinformatics
 
 
 
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Contact

 

+44 (0)20 7594 5212m.sternberg Website

 
 
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Location

 

306Sir Ernst Chain BuildingSouth Kensington Campus

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Summary

 

Publications

Citation

BibTex format

@article{Ainsworth:2016:nar/gkw1248,
author = {Ainsworth, D and Sternberg, MJE and Raczy, C and Butcher, SA},
doi = {nar/gkw1248},
journal = {Nucleic Acids Research},
pages = {1649--1656},
title = {k-SLAM: Accurate and ultra-fast taxonomic classification and gene identification for large metagenomic datasets},
url = {http://dx.doi.org/10.1093/nar/gkw1248},
volume = {45},
year = {2016}
}

RIS format (EndNote, RefMan)

TY  - JOUR
AB - k-SLAM is a highly e cient algorithm for the characterisa-tion of metagenomic data. Unlike other ultra-fast metage-nomic classi ers, full sequence alignment is performed allow-ing for gene identi cation and variant calling in addition toaccurate taxonomic classi cation. Ak-mer based methodprovides greater taxonomic accuracy than other classi ersand a three orders of magnitude speed increase over align-ment based approaches. The use of alignments to nd vari-ants and genes along with their taxonomic origins enablesnovel strains to be characterised. k-SLAM's speed allows afull taxonomic classi cation and gene identi cation to betractable on modern large datasets. A pseudo-assemblymethod is used to increase classi cation accuracy by up to40% for species which have high sequence homology withintheir genus.
AU - Ainsworth,D
AU - Sternberg,MJE
AU - Raczy,C
AU - Butcher,SA
DO - nar/gkw1248
EP - 1656
PY - 2016///
SN - 1362-4962
SP - 1649
TI - k-SLAM: Accurate and ultra-fast taxonomic classification and gene identification for large metagenomic datasets
T2 - Nucleic Acids Research
UR - http://dx.doi.org/10.1093/nar/gkw1248
UR - http://hdl.handle.net/10044/1/43100
VL - 45
ER -