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/**
* The GBS package provide plugins and analysis approaches for genotyping by sequencing.
*
* Genotyping-by-sequencing (GBS) is a reduced representation approach for sampling the genome.
* The approach dates back to 2000 and 2001, when the human genome was restricted
* and sequenced by Sanger.
*
* The TASSEL GBS pipeline grew out of a protocol developed out of efficient and
* inexpensive approach published in 2011.
* The TASSEL GBS PE(pair end) pipeline is used to improve physical alignment of GBS tags.
*
* Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE.
* (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species.
* PLoS One 6(5): e19379.
*
* The bioinformatics has developed substantially since then and a new publication describing
* the approaches is:
*
* Glaubitz JC, Casstevens TM, Lu F, Harriman J, Elshire RJ, Sun Q, Buckler ES. (2014)
* TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline. PLoS ONE 9(2): e90346.
*
* Key design principles:
* Observed sequences are calls READS. These reads are trimmed and combined into
* clusters of identical sequences called TAGS.
* The distribution of tags are scored across taxa (samples) and recorded in a Tags by Taxa object (TBT).
* The genetic and physical mapping of tags are recorded in a Tags On Physical Map (TOPM)
* object. Once SNPs are identified their positions are recorded in a TOPM, which
* can be used in a single step production calling pipeline.
*
*
* This effort was funded by the NSF Plant Genome, NSF BREAD program, and the USDA.
*
*/
package net.maizegenetics.analysis.gbs;