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The performance evaluation shows that CUSHAW2 is consistently among the highest-ranked aligners in terms of alignment quality for both single-end and paired-end alignment, while demonstrating highly competitive speed.
Using the above measures, CUSHAW2 is shown to be among the highest-ranked aligners in terms of alignment quality for both the SE and the PE alignment for a variety of error rates and varying amount of indel errors.
We found the "filtering" and "combined reference" strategies performed better than aligning reads directly to human reference in terms of alignment and variant calling accuracies.
A read is classified as unambiguously aligned (U set) if its best hit in terms of alignment score as has significantly better values of both as and hs than the second best hit; otherwise, it is discarded as ambiguously aligned (A set, so that | T | = | U | + | A | + | N |).
We suspect this is more about the type or length of training and that women athletes can learn something from dancers about the way they train, the precision of their balance and jumping in terms of alignment and frequency and duration of training.
It is determined that a device designed to have a large clear aperture of 15 μm would have an advantage in terms of alignment.
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Values from all gene transcript isoforms, as defined by UCSC, were summed to yield values in terms of alignments per million reads for each of the 29,416 genes.
The low programming current and the good dimensional control of the sub-lithographic features achieved with the μTrench structure are combined with a self-aligned patterning strategy that simplify the integration process in term of alignment tolerances and of number of critical masks.
In terms of read alignment, the two alignment methods produced almost the same FDR and FNR for all three strategies, except that the FNR was lower for the combined reference strategy when BWA was used.
In such a case, the first (in terms of time) alignment is selected, while the other alignments are discarded.
We have extended the previous "Benchmark RNA Alignment dataBase" BRAliBase II by a factor of 30 in terms of the alignment number and with respect to the range of sequences per alignment.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com