bio-polyploid-tools
Introduction
This tools are designed to deal with polyploid wheat. The first tool is to design KASPer primers, making them as specific as possible.
Installation
‘gem install bio-polyploid-tools’
Notes
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If the SNP is in a gap in the alignmetn to the chromosomes, it is ignored.
BUG: Sometimes the primers are reversed (the first comes second) BUG: Blocks with NNNs are picked and treated as semi-specific. BUG: If the name of the reference have space, the ID is not chopped. “>gene_1 (G12A)” shouls be treated as “>gene_1”. TODO: If reading from a reference file, only get one reference to align when the region is queried several times TODO: Add a parameter file file to tweak the alignments.