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For both alignments the minimum length of a block was 10 and gapped positions were included.
To evaluate the quality of new alignments of SVRs over the previous alignments, scores were computed for both alignments.
Variable and parsimoniously informative sites were determined for both alignments.
Standard sequence logos are identical for both alignments; however, CodonLogo is able to discriminate between the two situations.
For a true R500 IMB211 polymorphism, the majority of reads should match the appropriate allele for both alignments.
For both alignments we used a threshold α value of 0.001, a random sampling of 100000, and a bootstrap value of 100.
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An elaborate dual-triangle optical path design is applied to share one detector for both alignment and view.
For both alignment programs, gap opening and extension parameters were set to their defaults.
The figures for both alignment lengths are similar and present the same trends (slightly better for 600 bp for all methods, as expected), so we let the results on 300 bp for the Additional file 1.
> -wrap-foot> For both aligners, most wrong alignments are caused by overlooking alignments with a similar score to the best reported alignment.
Also calculated was a weighted alignment score for both BLASR and LAST alignments, taking the number of reads multiplied by mean identity (Additional file 1: Figure S4).
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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