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To help the process of assembly, reads are obtained with some long-range information.
Raw assembly reads were visualised and verified using the programme Hawkeye (Amos) [28].
For reference-based assembly, reads from each sample were mapped against the L. (V).
Since the proposed technique relies on de novo assembly, read length is critical for typing accuracy.
For SOAPdenovo assembly, reads were trimmed after the first base falling below Q7.
Prior to assembly, read quality was examined using FastQC v0.10.1 (Babraham Bioinformatics, 2014).
To validate the CLC assembly, reads were also passed through the Trinity de novo assembly pipeline using default parameters [ 28].
Following transcriptome assembly, reads were filtered, sorted, and prepared for NCBI transcriptome shotgun assembly (TSA) submission as previously described [ 8].
To maximize the breadth of the transcriptome assembly, reads sequenced from different segments were pooled prior to assembly.
To assess the completeness of the assembly, reads from short-insert size libraries were re-mapped onto the assembly.
For the fasted treatment partial assembly reads from the 454 plate that yielded average read lengths (400 bp) were used.
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