Fig. 6

Analysis of repeat sequences within different assemblies. SATFIND [23] was used on contigs >2.5 kb. The total length of each region of a repeated DNA sequence is plotted against the repeat’s unit length, for the WTSI genome assembly (a) and our final assembly (b). The orange and red lines are at 150 bp (typical maximum read length for an Illumina HiSeq run) and 650 bp, respectively. Any VeCTRs with a unit length longer than 150 bp would not be identifiable as a repetitive sequence on an Illumina sequencer. Any VeCTRs with a region length longer than the maximum target fragment length for Illumina sequencing (typically 650 bp) will be collapsed into a shorter region if only non-mate-paired 150 bp reads are used for the assembly. c Alignment of the region corresponding to the longest repeat unit length in (b), with each base represented as a colored line. Although the resolution of repeats is greatly improved compared to the WTSI assembly, such sequences still present a challenge for assembly, as evidenced by the fact that the 5' end of this sequence corresponds to a contig end (tig00023164; coordinates on the left). The color code is as in Fig. 4. Very long stretch of a complex tandem repeat (VeCTR), Wellcome Trust Sanger Institute (WTSI)