The consensus sequences were split into contigs at every occurrence of an 'N'.
Genomes were then decomposed into synteny blocks, and then the target genome was split into contigs, where each contig represents exactly one synteny block.
Thus, the low abundance filtered transcript assembly was split into contigs that contain complete open reading frames, contigs containing transcript fragments with predicted partial open reading frames, and contigs containing no ORF prediction.
Initially, the Newbler developers said that these contigs are not parts of actual transcripts and are therefore not reported, but we traced a few of these fragments and found that they were made up of well aligned, overlapping reads that had been split into contigs and then discarded.
However, if cutoff value is set too low, some real BAC contigs will be split into small contigs or singletons.
However, a real BAC contig could be split into two contigs or more when we use assembly parameters of high stringency, especially for those genome regions with higher levels of heterozygosity.
Whether a BAC contig is to be split into different contigs when assembly stringency is increased depends on the level of overlapping segments generated from restriction fingerprinting.
The 14,727 contig sequences in the Res.Image.fa file produced during the last IMAGE iteration were saved as they did not contain stretches of Ns, while the scaffold sequences had to be split into their constituent contigs before proceeding to resize the N stretches.
In these assemblies, batches of 500,000 Illumina reads were assembled de novo using gsAssembler, and contigs >2000 bp were split into shorter contigs (≤1,950 bp) with 100 bp overlaps.
