Fig 1.
Overview of the hybrid assembly pipeline.
Raw data generated by several NGS platforms are preprocessed into a common format, which is registered to the library. A data set used at each assembly stage can be specified separately. The assembly results are denoted according to the supplied data, as illustrated at the bottom of the figure.
Table 1.
Statistical information of input short read data.
Table 2.
Characteristic indices of the strands from several assemblies.
Table 3.
K-mer size dependence of the R50 valuesa of the A. oryzaeb unitigs.
Fig 2.
Dotplot alignments of assembled strands against the reference genome sequence of A. oryzae.
Alignments shorter than 4000 bp were omitted from the plots. Forward and reverse alignments are plotted in red and blue colors, respectively. The Roman numerals I-VIII on the abscissa are the chromosome index of A. oryzae. (a) The MSSH assembly, (b) the denovo2 assembly.
Table 4.
Characteristics of the A. oryzaea contigs/scaffolds/strands from several assembliesb.
Table 5.
Number of ORFs reproduced in the assemblies.
Table 6.
Number of SMB gene clusters reproduced in the assemblies.
Fig 3.
Dotplot alignments of assembled strands against the reference genome sequence of S. avermitilis.
Alignments shorter than 4000 bp were omitted from the plots. Forward and reverse alignments are plotted in red and blue colors, respectively. (a) The MSSH assembly, (b) the HHHH assembly.