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ChloroSeq specifications


Unique identifier OMICS_13081
Name ChloroSeq
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data RNA-Seq alignment data
Input format BAM, gff3
Output data Count tables
Output format TXT
Operating system Unix/Linux
Programming languages Perl, Shell (Bash)
Computer skills Advanced
Stability Stable
Source code URL
Maintained Yes


No version available



  • person_outline David Roy Smith <>

Publication for ChloroSeq

ChloroSeq citation


ChloroSeq, an Optimized Chloroplast RNA Seq Bioinformatic Pipeline, Reveals Remodeling of the Organellar Transcriptome Under Heat Stress

PMCID: 5015939
PMID: 27402360
DOI: 10.1534/g3.116.030783

[…] transcript analysis, organellar transcriptomes are rarely assessed even when present in published datasets. here, we describe the development and application of a rapid and convenient method, chloroseq, to delineate qualitative and quantitative features of chloroplast rna metabolism from strand-specific rna-seq datasets, including processing, editing, splicing, and relative transcript […]

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ChloroSeq institution(s)
Department of Biology, University of Western Ontario, London, ON, Canada
ChloroSeq funding source(s)
The Natural Sciences and Engineering Research Council of Canada (Discovery Grant)

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