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Maldonado E, Almeida D, Escalona T, Khan I, Vasconcelos V and Antunes A (2016)
LMAP: Lightweight Multigene Analyses in PAML.
BMC Bioinformatics, 17:354.
doi: https://doi.org/10.1186/s12859-016-1204-5
Enhanced tool for detecting CNVs from whole-exome sequencing data
... (WES) data to identify CNVs. EXCAVATOR2 enhances the identification of all genomic CNVs, both overlapping and non-overlapping targeted exons by integrating the analysis of In-targets and Off- targets reads.
EXCAVATOR2 can be effectively employed for the identification of CNVs in small as well as large-scale re-sequencing population and cancer studies.
EXCAVATO2 paper:
http://nar.oxfordjournals.org/content/early/2016/08/09/nar.gkw695.full?keytype=ref&ijkey=O8r64Qj81gfMzLo
...://ricediversity.org, and within the corresponding publications and how-to videos:
How to videos:
http://vimeo.com/cornellricelab
PANorama1.0 (Crowell et al. 2014):
http://www.plantphysiol.org/content/165/2/479.short
PANorama2.0 (Crowell et al. 2016):
(http://goo.gl/vQux5Z)