Mapping and further processing

We recommend using BWA-MEM to map short GBS reads to a reference sequence and to analyze the read depth distribution with SMAP delineate (available soon).

Single-digest GBS and single-end sequencing

_images/separately_SE_SD-GBS_SMAP_legend_2.png

Single-digest GBS and paired-end sequencing, mapped separately

_images/separately_PE_SD-GBS_SMAP_legend_2.png

Single-digest GBS and paired-end sequencing, merged

_images/merged_PE_SD-GBS_SMAP_legend_2.png

Double-digest GBS and single-end sequencing

_images/separately_SE_DD-GBS_SMAP_legend_2.png

Double-digest GBS and paired-end sequencing, mapped separately

_images/separately_PE_DD-GBS_SMAP_legend_2.png

Double-digest GBS and paired-end sequencing, merged

_images/merged_PE_DD-GBS_SMAP_legend_2.png