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These scaffolds were removed from the rest of the sequence data and the sequence of the circular genome was completed by manual assembly and PCR amplification of gap regions.
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SOLiD technology is well-suited for resequencing studies as it returns high volumes of data and the sequence-by-ligation strategy is able to distinguish sequencing errors from true nucleotide variants during alignment [ 47, 48].
We used the trio-based data and the sequencing data in binary format for our experiment.
To assess the 16S data using 27Fmod, we compared various 16S sequence and qPCR data obtained from two mock communities (Supplementary Table S3) that are useful to evaluate the quantitative accuracy of 16S-based data and the sequencing error rate.
∙ No critical issues emerged about the data workflow and the sequence of data input.
KKY acquired the genomic data and performed the sequence alignment.
CAH collected the genetic sequence data and performed the sequence alignment.
This will enable the user to query the 3DSwap knowledgebase using sequence data and retrieve the sequence homologs.
SNH participated in the microarray experiments, the microarray data analysis and the sequence analysis.
MS participated in the microarray data analysis and the sequence analysis.
LJH coordinated the microarray data analysis and the sequence analysis and contributed to the writing of the manuscript.
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