Is there a method or a tool to align/map a small number of contigs (obtained with Canu) to a subsequence extracted from a reference genome ? For example,in a similar way to reads to reference assembly (using bwa mem, bowtie, minimap, etc), I want to align/assemble 6 contigs that span a region of interest to the reference sequence and to visualize the mapping (using Tablet, IGV, UGENE, etc.) with the overlap regions and gaps.
Or, is it possible to assemble "de novo" only a small number of contigs (that cover a specific region) into a bigger scaffold and align the sequence obtained to a reference subsequence ?
Thank you !
Simply align using
minimap2. Are the contigs larger or smaller than the sub-sequence. Depending on size you could do the search by swapping the two i.e. using reference as query.