I am using short read data to map against assemblies as part of a bulk segregant analysis. The result varies significantly for certain contigs based on whether the reference is the individual contig or within the whole assembly.
Is there a tool which would allow me to map the entire short read dataset to each individual contig one after the other? (rather than to the complete assembly)
(i.e. perform the mapping for the first contig whilst ignoring the others and then remap the complete short read dataset to the next contig, then the next etc.)