Omics Tools
Abstract
The Omics Tools package provides several small trivial tools for work in genomics. This single portable package, the omics.jar file, is a toolbox that works in any Java-based environment, including PCs, Macs, and supercomputers. The number of tools is expected to grow. One tool (called cmsearch.hadoop or cmsearch.local), calls the external cmsearch program to predict non-coding RNA in a genome. The cmsearch program is part of the third-party Infernal package. Omics Tools does not contain Infernal. Infernal may be installed separately. The cmsearch.hadoop subtool requires Apache Hadoop and runs on a supercomputer, though cmsearch.local does not and runs on a server. Omics Tools does not contain Hadoop. Hadoop mat be installed separartely The other tools (cmgbk, cmgff, fastats, pal, randgrp, randgrpr, randsub) do not interface with third-party tools. Omics Tools is written in Java and Scala programming languages. Invoking the help command shows currently available tools, as shown below: schaumbe@gpint06:~/proj/omics$ java -jar omics.jar help Known commands are: cmgbk : compare cmsearch and GenBank Infernal hits cmgff : compare hits among two GFF (version 3) files cmsearch.hadoop : find Infernal hits in a genome, on your supercomputer cmsearch.local : find Infernal hits in a genome, on your workstation fastats : FASTAmore »
- Authors:
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1231738
- Report Number(s):
- OMICS.JFAR; 002975MLTPL00
R&D Project: YGBOM; 2014-066
- DOE Contract Number:
- AC02-05CH11231
- Resource Type:
- Software
- Software Revision:
- 00
- Software Package Number:
- 002975
- Software Package Contents:
- Software package available from Lawrence Berkeley National Laboratory at the following URL: https://bitbucket.org/berkeleylab/jgi-omics
- Software CPU:
- MLTPL
- Open Source:
- No
- Source Code Available:
- No
- Country of Publication:
- United States
Citation Formats
Schaumberg, Andrew. Omics Tools.
Computer software. Vers. 00. USDOE. 21 Dec. 2012.
Web.
Schaumberg, Andrew. (2012, December 21). Omics Tools (Version 00) [Computer software].
Schaumberg, Andrew. Omics Tools.
Computer software. Version 00. December 21, 2012.
@misc{osti_1231738,
title = {Omics Tools, Version 00},
author = {Schaumberg, Andrew},
abstractNote = {The Omics Tools package provides several small trivial tools for work in genomics. This single portable package, the omics.jar file, is a toolbox that works in any Java-based environment, including PCs, Macs, and supercomputers. The number of tools is expected to grow. One tool (called cmsearch.hadoop or cmsearch.local), calls the external cmsearch program to predict non-coding RNA in a genome. The cmsearch program is part of the third-party Infernal package. Omics Tools does not contain Infernal. Infernal may be installed separately. The cmsearch.hadoop subtool requires Apache Hadoop and runs on a supercomputer, though cmsearch.local does not and runs on a server. Omics Tools does not contain Hadoop. Hadoop mat be installed separartely The other tools (cmgbk, cmgff, fastats, pal, randgrp, randgrpr, randsub) do not interface with third-party tools. Omics Tools is written in Java and Scala programming languages. Invoking the help command shows currently available tools, as shown below: schaumbe@gpint06:~/proj/omics$ java -jar omics.jar help Known commands are: cmgbk : compare cmsearch and GenBank Infernal hits cmgff : compare hits among two GFF (version 3) files cmsearch.hadoop : find Infernal hits in a genome, on your supercomputer cmsearch.local : find Infernal hits in a genome, on your workstation fastats : FASTA stats, e.g. # bases, GC content pal : stem-loop motif detection by palindromic sequence search (code stub) randgrp : random subsample without replacement, of groups randgrpr : random subsample with replacement, of groups (fast) randsub : random subsample without replacement, of file lines For more help regarding a particular command, use: java -jar omics.jar command help Usage: java -jar omics.jar command args},
doi = {},
url = {https://www.osti.gov/biblio/1231738},
year = {Fri Dec 21 00:00:00 EST 2012},
month = {Fri Dec 21 00:00:00 EST 2012},
note =
}
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