ITEP pipeline

ITEP specifications

Information


Unique identifier OMICS_08610
Name ITEP
Alternative name Integrated Toolkit for Exploration of microbial Pan-genomes
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python, Shell (Bash)
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Requirements SQLite, MCL, NCBI BLAST+, BioPython, Numpy, Ruffus, ETE2
Maintained Yes

Versioning


Add your version

Maintainer


  • person_outline Than D. Price <>

Publication for Integrated Toolkit for Exploration of microbial Pan-genomes

ITEP citation

2017
PMCID: 5516251

[…] (12) and thermosulfurimonas dismutans (lwlg00000000) were retrieved from genbank. comparative genome analysis was performed with the integrated toolkit for exploration of microbial pangenomes (itep) (25) version 1.1 as follows. an itep sql database was generated by using standard cutoff values (blastp e-value cutoff, 1e-5; blastn e-value cutoff, 1). genes were clustered on the basis […]

ITEP institution(s)
Institute for Systems Biology, Seattle, WA, USA

ITEP review

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nick_youngblut

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Desktop
ITEP has pretty good documentation and support. Setup is pretty straight-forward, but it's not integrated into conda or other package managers. ITEP is great for creating a database that can be flexibly queried with piped bash commands. The software is probably limited to 100-200 microbial genomes. Thousands of genomes would probably take too many compute resources.