John Lees edited this page Aug 24, 2017 · 10 revisions

seer

Sequence element enrichment analysis.

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Find sequence elements (words/kmers) that are enriched in samples with a given phenotype, which may be binary or continuous.

See the usage and interpretation pages. There is also a tutorial.

If you are having trouble with installation or usage, first take a look at the FAQ and troubleshooting.

Published in Nature Communications:

Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes
John A Lees, Minna Vehkala, Niko Välimäki, Simon R Harris, Claire Chewapreecha, Nicholas J Croucher, Pekka Marttinen, Mark R. Davies, Andrew C. Steer, Steven Y. C. Tong, Antti Honkela, Julian Parkhill, Stephen D Bentley, Jukka Corander
http://www.nature.com/articles/ncomms12797

Publications seer has been used in:

  1. Weinert L a., Chaudhuri RR, Wang J, Peters SE, Corander J, Jombart T, et al. Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis. Nat Commun. 2015; 6: 6740. doi:10.1038/ncomms7740
  2. Chewapreecha C., Holden M. T. G., Vehkala M., Välimäki N., Yang Z., Harris S. R., et al. Global and regional dissemination and evolution of Burkholderia pseudomallei. Nat Micro 2017; 2: 16263. doi: 10.1038/nmicrobiol.2016.263
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