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In the same set of alignments, we scanned for the occurrence of CGIs in aligned regions.
Once CCS reads are sorted, the pipeline uses Bowtie2's default alignment (end-to-end read alignment) to align reads to the corresponding reference sequence and outputs a set of alignments in SAM format.
If the selected alignment was not fully representative of the assembly unit, we selected a set of alignments that was better representative of the assembly unit.
The representation is a compact graph that makes it easy to impose additional biological constraints and select one desirable alignment from the large set of alignments.
From this initial set of alignments, 205 reads were found to meet these criteria.
The total set of alignments was processed as follows.
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Our Tesla had been modified with an additional set of alignment wheels — sticking out in front like a pair of ears.
With gratitude to Hugo Cory, who helped me clearly see the hilarious horror of my behavior, and John Friend, whose elegant, concise set of alignment principles called the Universal Principles of Alignment™ shall inspire these posts in some way.
The Fhom Estimator helps determine a specific E-Value cutoff for a particular set of alignment hits, above which the number of homologs is negligible.
These set of alignment-free measures are usually called D-type statistics.
These were calculated for all competitive assemblies using the set of scaffold lengths and the set of alignment lengths of the scaffolds to the VFRs.
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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