Title

Authors

Affiliation

¹Department of Biology, ²The Center for Genomic Advocacy, Indiana State University 600 Chestnut Street, Terre Haute, IN 47809, U.S.A

Email

Yongsheng.Bai@indstate.edu; *Corresponding author

Article Type

Software

Date

Received November 18, 2014; Accepted November 19, 2014; Published November 27, 2014

SNPAAMapper, a genome-wide SNP downstream analysis and annotation pipeline, was designed to classify detected variants according to genomic regions and report the mutation class by processing whole-genome and/or whole-exome sequencing data. A widely used sequence and data annotation table format “knownGene.txt” has not yet been created for many popular model organisms (e.g. Arabidopsis). Instead, NCBI .tbl annotation format files are provided for these species. Therefore, it is of interest to describe SNPAAMapperT2K, a genome-wide SNP downstream analysis and annotation pipeline for species annotated with NCBI .tbl data files (e.g. Arabidopsis). The pipeline is tested with a deeply sequenced Arabidopsis thaliana strain (Seattle-0). The SNPAAMapperT2K can also annotate and report SNP classes for other species, whose chromosome files are annotated as NCBI .tbl format, but do not have their annotated knownGene.txt files available.

Availability

Perl scripts and required input files are available on the web at http://isu.indstate.edu/ybai2/SNPAAMapperT2K

Citation

Bai, Bioinformation 10(11): 711-715 (2014)
 

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.