To assess the quality of the resulting assembly, we assembled the data using the direct overlap algorithm and compared the contigs to the reference.
Whenever an assembler incorrectly merges two contigs, the resulting assembly will seem to have a bigger N50 size, thus creating an inferior assembly with an apparently 'better' N50 size.
Although Newbler alone was able to assemble the reads into five scaffolds, the resulting assembly had a considerable number of degenerate positions which could not be resolved just from an error correction step using Illumina reads (Table 3).
Reads were first assembled in MIRA v3.0rc4 [ 55] and the resulting assembly was passed through a second assembly step in CAP3 [ 56] to join additional contigs (Table 2).
SMRT reads were assembled by the Biosciences Division at Oak Ridge National Laboratory (Oak Ridge, Tennessee, United States) and the resulting assembly was used as a reference genome for methylome analysis, which was carried out by Pacific Biosciences (Menlo Park, California, United States).
Thus, for this genome, the choice of assembler seems to have a large impact on the quality of the resulting assembly.
The completeness of the resulting assembly was estimated using 1,007,962 ESTs from BRASUZ1.
The large N25 (6,431 bp), N50 (3,483 bp) and N75 (1,116bp) values of the resulting assembly were indicative of its success.
The resulting assembly of multiple acceptors surrounding a donor permits this construct to exhibit high resonance energy transfer efficiency (∼64.8%).
We show that the information provided by aligning the whole-genome shotgun reads of the target against a reference genome can be used to substantially improve the quality of the resulting assembly.
A constraint-based approach is used to confirm that the resulting assembly sequence is both feasible and practical and also gives guidance on the quality of the sequence.
