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Aptaligner's complexity is O NMM), similar to pairwise alignments, where N equals sequence length and M equals the library length.
The Illumina Genome Analyzer (Illumina, Inc) was used with paired-end reads of 36 bp, a mean library length of 220 and a standard deviation of about 20.
Notably, there was little variation in the rate at which reads were filtered due to error correction and haplotype differences as the library length increased.
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Library lengths and sequencing parameters are listed in supplementary table S2, Supplementary Material online.
Specifically, we prove that optimal detection and resolution of breakpoints is achieved using a mix of exactly two insert library lengths.
The average library lengths of approximately 500 bp were estimated from profiles on a Bioanalyzer 2100 (Agilent) with DNA HS Assay.
This program provided criteria for assessing the quality of the SAGE libraries (length distribution of ditags, frequency of replicate ditags, and detection of linkers).
Few bacterial groups were found in grapevine tissues using a diverse array of methods including 16S rRNA gene libraries, length heterogeneity PCR, and FISH hybridization [ 4, 9, 57].
Therefore, the overall libraries lengths are usually designed to be less than 150 bases in total length, including a random region of 20 to 80 bases, and are chemically synthesized using phosphoramidite chemistry [ 3].
This offset can be calculated as mean library fragment length minus insertion vector length.
Variance in library insert length is also a critical factor here and should be minimized to the greatest degree possible.
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