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Yet Another Tool Suite for analyzing RNA-seq derived transcriptome YeATS

A methodology that replicates and improves existing methodologies, and implements a workflow for error estimation and correction followed by genome annotation and transcript abundance estimation for RNA-seq derived transcriptome sequences. YeATS unique feature is the upfront determination of the errors in the sequencing or transcript assembly process by analyzing open reading frames of transcripts. YeATS identifies transcripts that have not been merged, result in broken open reading frames or contain long repeats as erroneous transcripts.

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YeATS classification

YeATS specifications

Software type:
Toolkit/Suite
Restrictions to use:
None
Input format:
FASTA
Programming languages:
Perl
Computer skills:
Advanced
Stability:
Stable
Interface:
Command line interface
Input data:
A set of post assembly transcripts
Operating system:
Unix/Linux
License:
GNU General Public License version 3.0
Version:
2.0
Maintained:
Yes

YeATS distribution

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YeATS support

Documentation

Maintainer

  • Sandeep Chakraborty <>

Credits

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Publications

Institution(s)

Plant Sciences Department, University of California, Davis, CA, USA; UC Davis Genome Center Bioinformatics Core Facility, University of California, Davis, CA, USA; Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA; Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhaba Road, Mumbai, India; USDA Forest Service Hardwood Tree Improvement and Regeneration Center, Purdue University, West Lafayette, IN, USA

Funding source(s)

This work was supported by support by the California Walnut Board and UC Discovery program.

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