Supplementary Figure 3: Creation of merged and concatenated reads.
From: epiGBS: reference-free reduced representation bisulfite sequencing
(a) A typical epiGBS library shows a peak on a Bioanalyzer image corresponding to fragments of ~300 basepairs (bp), although larger fragments are also obtained. A 300 bp fragment corresponds to an epiGBS fragment (insert) of 163 bp, as adapters are not sequenced. (b) Barcoded adapters A and B can be ligated on both ends of each fragment, so for any given genomic locus both forward and reverse oriented inserts exist. Fragments derive from either Watson or Crick strand. (c, d) Overlapping paired-end reads are merged whereas non overlapping paired-end reads are concatenated to facilitate de novo reference reconstruction. Concatenation is performed by adding 10 N’s between the forward and reverse read. Concatenated reads can be used to determine the sequence on both ends of inserts larger than ~1,9x the read length.
