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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


No version available

Maintainer


  • person_outline Than D. Price

Publication for Integrated Toolkit for Exploration of microbial Pan-genomes

ITEP citations

 (15)
library_books

Diversification of Secondary Metabolite Biosynthetic Gene Clusters Coincides with Lineage Divergence in Streptomyces

2018
PMCID: 5872123
PMID: 29438308
DOI: 10.3390/antibiotics7010012

[…] ere annotated using the online RAST Server []. Multiple whole genome alignments were obtained with Mugsy [], and trimAL v1.2 removed poorly aligned regions []. Orthologous genes were identified using ITEP [] with MCL clustering parameters as follows: inflation value = 2.0, cutoff = 0.04, maxbit score. Average nucleotide identity (ANI) was determined using mother []. Genome sequences are available […]

call_split

Metagenomic investigation of vestimentiferan tubeworm endosymbionts from Mid Cayman Rise reveals new insights into metabolism and diversity

2018
Microbiome
PMCID: 5787263
PMID: 29374496
DOI: 10.1186/s40168-018-0411-x
call_split See protocol

[…] Integrated Toolkit for the Exploration of Microbial Pangenomes (ITEP, []) was used to profile Genbank files that had been generated using the RAST pipeline [] from the MAGs identified in this study and five published symbiont genomes assembled from three other tub […]

library_books

PGAP X: extension on pan genome analysis pipeline

2018
BMC Genomics
PMCID: 5780747
PMID: 29363431
DOI: 10.1186/s12864-017-4337-7

[…] fungi [], and plant []. To make pan-genome analysis for bacterial genomes more easy and efficient, several programs and databases were developed, including Panseq [], PGAT [], PanCGHweb [], PanGP [], ITEP [], PGAP [], and so on. Early programs or databases mainly focus on limited functional analysis, while PGAP integrates five common analytical modules, including cluster analysis of functional gen […]

call_split

Linking pangenomes and metagenomes: the Prochlorococcus metapangenome

2018
PeerJ
PMCID: 5804319
PMID: 29423345
DOI: 10.7717/peerj.4320
call_split See protocol

[…] similarities of each amino acid sequence in every genome against every other amino acid sequence using blastp (), (2) removes weak hits using the ‘minbit heuristic’, which was originally described in ITEP (), to filter weak hits based on the aligned fraction between the two reads, (3) uses the MCL algorithm () to identify gene clusters in the remaining blastp search results, (4) computes the occur […]

library_books

Methanogenesis in oxygenated soils is a substantial fraction of wetland methane emissions

2017
Nat Commun
PMCID: 5691036
PMID: 29146959
DOI: 10.1038/s41467-017-01753-4

[…] me (Supplementary Data ) as a model and are included in the Supplementary Note . To identify unique gene features in reconstructed genomes that differ from isolate Methanothrix genomes, we created an ITEP database and compared all genes via all vs. all blast, orthoMCL clustering and sqlite database generation. A cluster is defined as having bidirectional best hits based on a percent identity cutof […]

call_split

Genomic variation in microbial populations inhabiting the marine subseafloor at deep sea hydrothermal vents

2017
Nat Commun
PMCID: 5655027
PMID: 29066755
DOI: 10.1038/s41467-017-01228-6
call_split See protocol

[…] vum sp. AR, Sulfurovum sp. NBC7-1, Sulfurovum G1, and Sulfurovum lithotrophicum ATCC BA797). For sequence-based comparison, we used the Integrated Toolkit for the Exploration of microbial Pangenomes (ITEP) to conduct MCL clustering and comparison of ORFs that had been identified using the RAST pipeline. We clustered ORFs using an inflation value of 2 and a maxbit score of 0.3. We used RPSBLAST to […]

Citations

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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.