Assemblathon 1: a competitive assessment of de novo short read assembly methods
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Figure 1 — The phylogeny of the simulated haploid genomes. The root genome derives from human chromosome 13. The α1 and α2 haplotypes form the diploid genome from which we generated reads. The β1 and β2 haplotypes form a diploid out-group genome that was made available to the assemblers. 
Figure 2 — N50 statistics. Assemblies are sorted left to right in descending order by scaffold path NG50. Data points for each assembly are slightly offset along the x-axis in order to show overlaps. 
Figure 3 — An adjacency graph example demonstrating threads, contig paths and scaffold paths. Each stack of boxes represents a block edge. The nodes of the graph are represented by the left and right ends of the stacked boxes. The adjacency edges are groups of lines that connect the ends of the stacked boxes. Threads are represented inset within the graph as alternating connected boxes and coloured lines. There are three threads shown: black, gray and red. The black and gray threads represent two haplotypes, there are many alternative haplotype threads that result from a mixture of these haplotype segments which are equally plausible given no additional information to de-convolve them. The red thread represents an assembly sequence. For the assembly thread consistent adjacencies are shown in solid red. The dashed red line between the right end of block g and the left end of block i represents a structural error (deletion). The dashed red line between the right end of block k and the left end of block m represents a scaffold gap, because the segment of the assembly in block n contains wild card characters. The example therefore contains three contig paths: (from left to right) blocks a…g ACTGAAATCGGGACCCC; blocks i, j, k GGAAC; and block m CC. However the example contains only two scaffold paths because the latter two contig paths are concatenated to form one scaffold path. Download 1.22 Mb. Share with your friends:
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