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Sequencing instrumentation continues to improve, allowing more reads at lower costs.
On all the considered datasets, MTR discards a significantly smaller number of reads than LCA and it assigns much more reads at lower taxonomic ranks.
Finally, for RelocaTE to call a nonreference insertion event, there must be two or more reads, at least one left flanker and one right flanker, with a perfect overlap of the TSD, in the correct orientation, when the reads are aligned to the the reference.
However, this argument is currently less valid as the Illumina short-read sequencing technology, which produces many more reads at a lower cost per base, has been recently shown to be useful and accurate in de novo transcriptome assembly of non-model organisms [ 30].
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Seed-extend-based techniques in contrast usually map more reads at large edit distances but require more CPU time.
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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