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. 2014 May 22;15(1):394. doi: 10.1186/1471-2164-15-394

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© Yang et al.; licensee BioMed Central Ltd. 2014

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.

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High-throughput next generation sequencing of fast annealing DNA treated by S1 nuclease. (A) Sequencing library construction. We prepared samples for sequencing based on efficient intrastrand base pairing of palindromes. Briefly, the genomic DNA was denatured and rapidly reannealed. After single-strand specific S1 nuclease digestion, DNA was extracted by phenol-chloroform and libraries were prepared for 454 and Illumina sequencing. (B) Data analysis. 1: Mapping of unique reads to human reference genome (NCBI36/hg18). Black lines represent mapped unique reads. Hatched rectangles represent regions masked by RepeatMasker (M). 2: Assembly of uniquely mapped reads to identify contiguous regions (contigs, black rectangles), and calculation of base read ratio (B) of each contig. For a contig region “c” with n mapped reads, . 3: Clustering two or more contigs with a base read ratio >1.5 that are within 7.5 kb of each other to make a joined contig. 4: Determining Rank “R” that is the sum of all read lengths in the joined contig divided by the length of the joined contig minus the masked regions .

Inline graphic — High-throughput next generation sequencing of fast annealing DNA treated by S1 nuclease. (A) Sequencing library construction. We prepared samples for sequencing based on efficient intrastrand base pairing of palindromes. Briefly, the genomic DNA was denatured and rapidly reannealed. After single-strand specific S1 nuclease digestion, DNA was extracted by phenol-chloroform and libraries were prepared for 454 and Illumina sequencing. (B) Data analysis. 1: Mapping of unique reads to human reference genome (NCBI36/hg18). Black lines represent mapped unique reads. Hatched rectangles represent regions masked by RepeatMasker (M). 2: Assembly of uniquely mapped reads to identify contiguous regions (contigs, black rectangles), and calculation of base read ratio (B) of each contig. For a contig region “c” with n mapped reads, . 3: Clustering two or more contigs with a base read ratio >1.5 that are within 7.5 kb of each other to make a joined contig. 4: Determining Rank “R” that is the sum of all read lengths in the joined contig divided by the length of the joined contig minus the masked regions .