SEAR pipeline

SEAR specifications

Information


Unique identifier OMICS_19599
Name SEAR
Alternative name Search Engine for Antimicrobial Resistance
Interface Web user interface
Restrictions to use None
Input data Files from metagenomic, metatranscriptomic or isolate sequencing.
Input format FASTQ
Computer skills Basic
Stability Stable
Source code URL http://computing.bio.cam.ac.uk/sear/SEAR_WEB_PAGE/SEAR.html#download
Maintained No

Maintainer


This tool is not maintained anymore.

Information


Unique identifier OMICS_19599
Name SEAR
Alternative name Search Engine for Antimicrobial Resistance
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl, R, Shell (Bash)
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Will Rowe <>

Publication for Search Engine for Antimicrobial Resistance

SEAR IN pipeline

2017
PMCID: 5437528
PMID: 28175320
DOI: 10.1093/jac/dkx017

[…] nucleotide archive study with accession numbers prjeb12083 (metagenomes) and prjeb12284 (metatranscriptomes) (table 1). , args were identified in metagenomes and metatranscriptomes using the sear with default parameters.11 mge detection was carried out on all metagenomes as in rowe et al.10 (2016). briefly, reads were mapped to a custom mge database using bwa-mem (default options),15 […]

SEAR institution(s)
Department of Veterinary Medicine, University of Cambridge, Cambridge, UK; Wellcome Trust Sanger Institute, Cambridge, UK; Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK; Environment, Health and Safety, GlaxoSmithKline, Ware, UK
SEAR funding source(s)
Supported by GlaxoSmithKline, the Centre for Environment, Fisheries and Aquaculture Science and the Biotechnology and Biological Sciences Research Council.

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