Fig. 1

The introduction of palindromes by whole-genome amplification (WGA) and correction of these sequences with Pacasus. The colored squares in this figure indicate the four different nucleotides. In whole-genome amplification a DNA-polymerase binds to the DNA and starts making a copy of that strand (left-side of the image). Palindromes are introduced when during WGA the DNA-polymerase continues with elongation (indicated by the arrow) along an already created WGA product (a), generating a palindrome. In this example this incorrect elongation occurs several times (b), resulting in a DNA fragment containing four copies of the original fragment (c), which is sequenced. Pacasus detects the palindrome sequence by aligning the read’s reverse complement to itself (d) and splits the read in two smaller reads at the center of the alignment (split 1). This process is repeated and splits the two resulting reads again (split 2), yielding four separate, ‘clean’, reads. The full set of reads, corrected and left intact, is then used in, for example, read mapping or de novo assembly