Aziz Mithani^1,2, Eric J Belfield¹, Carly Brown¹, Caifu Jiang¹, Lindsey J Leach^1,3 & Nicholas P Harberd^1
1Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
²Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, D.H.A, Lahore 54792, Pakistan
³School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK

HANDS stands for "HSP base Assignment using NGS data through Diploid Similarity" and is a tool to characterize Homeolog-Specific Polymorphisms (HSPs) in allopolyploid genomes. HSPs are the positions in a polyploid genome where the homeologous subgenomes have different bases. HANDS uses the sequencing alignment/mapping (SAM) file of the polyploid genome (for example, bread wheat) obtained using sequence alignment tools such as Burrows-Wheeler Aligner along with the variants lists (HSPs for the polyploid and single base substitutions (SBSs) for the progenitor-relative diploids) to assign base-identity to the polyploid subgenomes. The variant lists are tab-separated files containing sequence name, position, reference base and consensus base, and can be generated using tools such as SAMtools. For queries regarding HANDS tool, please contact Aziz Mithani at aziz.mithani@lums.edu.pk

Download

HANDS can be downloaded from here.

Usage:

Input Parameters

-h or -help	Display this help
-s <File>	Polyploid SAM file
-g <File>	GFF file containing gene start/end coordinates
-hsp <File>	Polyploid HSP file
-snp1	Diploid 1 SNP file
-snp2	Diploid 2 SNP file
-snp3	Diploid 3 SNP file
-bd	Polyploid Base Distribution file (optional)
-bd1	Diploid 1 Base Distribution file (optional)
-bd2	Diploid 2 Base Distribution file (optional)
-bd3	Diploid 3 Base Distribution file (optional)
-out1	Genome 1 output file
-out2	Genome 2 output file
-out3	Genome 3 output file
-sp <float>	SNP pair proportion threshold (Default: 0.05)
-pm <float>	Base pattern matching threshold (Default: 0.5)
-r <Boolean>	Rectify Assignment using reference genome (Default: FALSE)
-d <int>	Use genome 2 as distant genome (Default: TRUE)

Examples:

To run the example data, go to the directory where you have extracted the files and run the following command.
By default, genome 2 is designated as a distant genome. This can be turned off by using parameter “-d” as shown below.
Pre-processing (validation of HSPs and SBSs) can be turned off by not providing the base distribution files.