PolyGembler¶

Description¶

polyGembler is for construction of genetic linakge maps or chromosomal-scale pseudomolecules combining de novo genome assembly and genetic mapping. The method assumes availability of genome-wide genotyping data such as GBS, RAD-seq and SNP array data, collected on a F1 outbred mapping population, as well as high coverage (i.e. greater than 30X) whole genome sequence data on a reference sample, or alternatively the availability of a set of reference contigs or scaffolds. By mapping marker set to contigs, polyGembler infers contig haplotypes for each sample. Contig haplotypes are then used to infer linkage groups corresponding to chromosomes as well as the optimal ordering of contigs within these chromosomes.

Environment Modules¶

Run module spider polygembler to find out what environment modules are available for this application.

Environment Variables¶

HPC_POLYGEMBLER_DIR - installation directory
HPC_POLYGEMBLER_BIN - executable directory

Categories¶

phylogenetics