GenomePeek specifications

Information


Unique identifier OMICS_24014
Name GenomePeek
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Katelyn McNair

Publication for GenomePeek

GenomePeek citations

 (2)
library_books

Draft Genome Sequences of Five Enterococcus Species Isolated from the Gut of Patients with Suspected Clostridium difficile Infection

2017
Genome Announc
PMCID: 5477334
PMID: 28522725
DOI: 10.1128/genomeA.00379-17

[…] sembled using a De Bruijn graph strategy as implemented in SPAdes 3.8 (). Genome coverage was 48 to 173× (median = 109×). We interrogated the resulting contigs for evidence of contamination using the GenomePeek web server and found no evidence of contaminating DNA (). We annotated the assembled genome sequences using the NCBI Prokaryotic Genome Annotation Pipeline (released 2013) (). Information a […]

library_books

Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition

2014
PeerJ
PMCID: 4145072
PMID: 25177534
DOI: 10.7717/peerj.520

[…] The 16S rRNA, rpoB, and recA gene sequences were extracted from the unassembled reads of each genome using the program genomePeek (K McNair, RA Edwards, 2014, unpublished data). Each group of sequences extracted from the same genome library were assembled into contigs using Newbler 2.7 () with default parameters. The […]

GenomePeek institution(s)
Department of Computer Science, San Diego State University, San Diego, CA, USA; Department of Biology, San Diego State University, San Diego, CA, USA; Computational Sciences Research Center, San Diego State University, San Diego, CA, USA; Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA
GenomePeek funding source(s)
Supported by grants from the National Science Foundation [DBI-0850356, MCB-1330800, and DEB-1046413].

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