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The first data set of Sanger reads consists of three bacterial genomes: Brucella suis [29], Wolbachia sp. [30] and Staphylococcus epidermidis RP62A [31].
Our computational procedure for the identification of GVs based on 454 reads consists of two steps.
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The transcriptome of C. cladosporioides MD2 was sequenced with Illumina sequencing technology to generate 19,776,638 raw reads consisting of 1,779,897,420 nucleotides (nt).
The 375,619 reads consisted of two independent 454 runs each covering half a plate.
The genome sequence of strain M1 obtained from paired end reads, consisted of 18 contigs that were oriented using in-house perl scripts, and then assembled into a complete genome using directed PCR.
A total of 654,159 reads consisting of nearly 165 Mb were obtained (Table 1).
These 119 million usable reads consisted of 17.6 million unique tags.
Longer reads consisting of 50−100 nt provided little additional benefits on the U regions extent.
Cloning errors resulted in 40,622 unique tags (11.0% or 413,837 sequence reads) consisting of only 5'and 3' adaptor sequences.
The F. noatunensis subsp. orientalis Toba04 strain was sequenced using 454-pyrosequencing [ 35] generating 263,717 reads consisting of 56,522,682 bases.
Therefore, informative reads consisted of reads representing the transgene as well as reads representing the endogenous mouse Prnp locus (Additional file 3).
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