The Oases pipeline receives as input a preliminary assembly produced by the Velvet assembler (Zerbino and Birney, 2008) which was designed to produce scaffolds from genomic readsets.
Those size thresholds were chosen based on analysis of a preliminary assembly in which all reads within those size ranges failed to assemble, supporting the interpretation that they might represent sequencing artifacts.
In this paper the packaging design is also presented and materials for flexible sensor array preliminary assembly are described.
Our preliminary assembly of the ACFR02 data identified 583 contigs that sum to 4.4 Mb of unique genome sequence, encoding 5,203 predicted proteins.
The designed arrays encompass part of the chromosomes 4, 7, 14, and 17 from the August 2007 preliminary assembly release with a median probe spacing of 409 bp.
Copy number regions were discarded if (1) they overlapped more than one contig and (2) contained gaps due to the high error rate of this preliminary assembly.
From that preliminary assembly, 13x was the mode of the contig coverage distribution, and 7x was chosen as just above half the previous value.
Segmental duplications have been mapped in the genomes of human [35], chimpanzee [36], and mouse [37], but the incomplete and highly error-prone preliminary assembly of the pig genome prevents us from drawing such a map.
Since our analytical pipeline for measuring the pig CNV landscape was developed in order to minimize the detection of somatic CNVs and false positives, and since the pig preliminary assembly contains high amounts of unfinished sequence and incorrectly mapped regions, our results are an obvious underestimate of the total number of CNVs in the sequences covered.
However, the largest family in the mammalian MRCA to eventually go extinct in any lineage (11 genes) is a V2R vomeronasal receptor gene family that has >100 genes in each rodent lineage but is absent from the dog, human, and chimpanzee genomes (it is, however, present in the preliminary assembly of the rhesus macaque genome; see Materials and Methods).
The 58,894 end sequenced BACs were then aligned with a preliminary assembly of the shotgun sequence of the Brachypodium genome (http://www.brachypodium.org/), comprising 1015 super-contigs (SC) representing 260 Mb without gaps, of which 17 were longer than 1 Mb and represented 99% of the genome sequence.
