Prerequisite Files for Lep Anchor
The Lep-Anchor modules, if you choose to run them, will require:
This is a fasta file of the genome you wish to anchor/orient. It's the one you used to map your samples to in order to generate the markers that fed into Lep-Map3.
The individual maps for each linkage group are found in the 7_*/ folders after the Lep-Map3 modules. LepWrap will concatenate the maps from 7_Intervals/ or 7_Distances/ into a single file depending on the data type you configure. If you generated these outside of LepWrap, then the file needs to be named lepanchor.input in a directory named 10_PlaceAndOrientContigs, like so: 10_PlaceAndOrientContigs/lepanchor.input. It should be a single file containing all the linkage groups. Make sure to specify in the config file if this file is distance or interval data.
This is a PAF file generated by minimap2 of your long reads mapped to your reference assembly (#1). The file is optional, but if you have the means to generate it, I would recommend it, as it can help anchor/orient the assembly.
