We tested our assembler using simulated reads from D. melanogaster and human chromosomes 1, 11, and 21, and produced assemblies with large sets of contiguous sequence and a misassembly rate comparable to other draft assemblies.
exSPA nder produced assemblies with the highest NG50 and largest assembled contig/scaffold.
Among the three assemblies, ABySS and CLCbio produced assemblies with better contiguity; they had fewer scaffolds (CLC: 1402 and Ab: 1490) with greater N50 (Ab 14550, CLC 14519) and both covered 96% of the Genbank reference genome sequence.
Three BAC clones that were previously sequenced and assembled using Sanger sequencing technology were aligned to the existing and newly produced assemblies for validation.
Read mapping to the Morex reference assembly with TopHat and Cufflinks produced assemblies of more than 40 million reads per library with an average of 70x per-base coverage.
When considering the number of errors, including local errors, ABySS and SGA consistently produced assemblies with the fewest errors.
When examining the number of contigs, mean, max, and N50 numbers, the Ion Torrent hybrid assemblies produced assemblies that were demonstrably superior to the MiSeq assemblies.
Similarly, ABySS produced assemblies with high number of misassemblies for the single-cell data.
However, another C.multidentata siphosome sample produced assemblies with large numbers of relatively short sequences (data unpublished).
These assemblers have different running time and memory requirements; and produce assembly results with varying quality.
We describe the algorithmic techniques used to produce assembly instructions given object geometry, orientation, and optional grouping and ordering constraints on the object's parts.
