As shown in Table 1, the general features of the contig assembly from the two libraries are similar: a total of 9,936 and 9,417 contigs were obtained from the viruliferous and naïve datasets, with average lengths of 376 bps and 362 bps, respectively.
In the present study, we compared the assembly from the three most frequently used assemblers, i.e. MIRA, Newbler v2.5.3, and Cap3 [ 30], since Velvet and ABySS are not developed for relatively long sequence assembly.
The better assembly result from the two read sets was determined based on contig and scaffold size statistics.
(This system began in the Greek-speaking provinces, long used to wooing their rulers with divine honours. It penetrated the west only slowly, but from 12 bc an assembly for the three imperial Gallic provinces existed at Lugdunum).
To detect SNPs in the cDNA pool, the consensus assembly sequence generated from the two trancriptome libraries was employed as a reference sequence to which individual reads were aligned using SOAPsnp [ 64].
Assembled transcripts from the six assemblies were aligned to the draft reference sequence using BWASW with default parameters (a mode of BWA) [ 20], and the numbers of covered bases for the diploid sequence were calculated as shown in Table 8.
Taking into account only the reliable region of the htt sequence identified in the v2.0 assembly, the gene structure obtained from the two assemblies of C. intestinalis was identical, except for the length of few introns and the lack of the last 400 nt of the longest 3'UTR in the v1.95 assembly.
The consensus assembly from all the five samples generated a total of 36 966 contigs with the average length of 1265 bp and N50 length of 1761 bp (Supplementary Table S3).
Even if only one individual is used for RNA-Seq, the assembly of related transcripts from the two sets of chromosomes creates "haplotypes" that do not exist, and this alone prohibits assembly of full-length transcripts from multiple sequences.
To discover SNPs in the 30% of the porcine genome not represented in the assembly, the 454 sequences from the two AluI libraries were used.
