..., BAM, FASTA, BED files or Chromosome size file (two-column, plain text file). Visualization can be performed by genome browsers like UCSC, IGB and IGV. However, R scripts can also...
...p? or other map (RAD-tag based). (software?)
BioNanoGenomics can be used for QC also
Use a genome browser to get a feeling for your results, e.g. IGV; add assembly, BAM files, ann...