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We used the MosaikAligner in the "all" alignment mode with a hash size of 13 and 20 bp as alignment candidate threshold, allowing a maximum of 4 mismatches.
Alignment candidate threshold (minimal alignment length to map the read) was optimized with hash size 20.
In parallel to hash size, time needed for the analysis decreased with the increased alignment candidate threshold.
Hash size (k-mer length for alignment) was optimized first without any limitation of alignment candidate threshold.
When the alignment candidate threshold is set, only alignments reaching at least the set length are considered.
Moreover, the fitting algorithm automatically selects a small set of candidate threshold values without any a priori information about their location.
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Calculation of candidate thresholds excludes these values.
However, the sensitivity of sequence alignment remained stable for alignment candidate thresholds up to half of the read length in our case (50 bp).
"If they could, I would have turned all the people over," Mr. Giuliani said in the interview, which was given for the new book "Meet the Next President: What You Don't Know About the Candidates" (Threshold Editions), by Bill Sammon, a reporter for The Examiner.
Then, the optimal solution is found among the candidate detection thresholds.
For each wavelet coefficient candidate to thresholding, T is calculated by comparing the sum of neighboring coefficients to λ.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com