Because the input DNA was sheared to a modal length of ∼160 bp, paired sequences were joined into overlapping extended contigs using FLASH (Magoč and Salzberg, 2011) with default settings.
Positive probes were joined into a single TAR if (1) they were adjacent (maxgap=0 bp, no intermittent non-positive probe) and (2) the length was at least 45 bp (minrun=45, mid-point first positive probe to mid-point last positive probe, resulting in at least 3 adjacent positive probes for a TAR).
The light 29x coverage reflected some 76% of the genome, and contigs assembled with Ray and SOAPdenovo were joined into scaffolds of modest size (N50 ~19.5 kb) using two insert libraries (300 bp and 2.5 kb inserts).
Neighbouring enriched tiles are joined into domains by requiring a minimal run of 1.6 kb or 400 bp and allowing a maximal gap of 800 or 200 bp for data obtained using the chromosome 4 or whole-genome arrays, respectively.
This resulted in 290 contigs (≥500 bp; N50 117,280 bp) that were joined using the Roche 454 paired-end reads to give 35 scaffolds.
These gaps were closed by direct PCR methods, and the scaffolds were joined together into the first assembly sequences over 3 947 535 bp in length, covering 99.09% of the genome.
The two fragments were joined by overlapping PCR using primers DC348 and DC351 to generate a 2,020 bp product that was cloned into pDCW88 [ 28] using the Kpnl and EcoRI sites.
Sequences lacking homology were joined by NHEJ, while asymmetric recombination is accompanied by repeat sequences longer than 50 bp [ 7].
Sequences from each end were joined following Q25 quality trimming of the ends followed by reorienting any 3′ 5′ reads back into 5′ 3′ and removal of short reads (<150 bp).
If a bop is less than 100 bp, it is joined to the previous bop, thus generating a bop of up to 300 bp.
