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9. Unusual matching mode (F refers to align with forward sequence, R refers to align with reverse sequence).
Mutation Surveyor software (MS; Softgenetics, State College, PA) version 4.0.5 was used in batch-mode with default parameters to align ab1 files to target reference sequence and make genotype calls.
The BWASW mode in BWA was used to align assembled transcripts into the draft diploid reference with default parameters [ 20].
We further aligned reads using the 'single-end' mode to identify potential short indels and structural variation.
For the (SAV) and the (SVO) samples, we tried to align both modes as accurately as possible, as was verified by manual inspection of the signals.
On the other hand, the transmission geometry of this dual-mode lensfree microscope is easier to align and operate, and in addition, it achieves a much larger imaging field-of-view (FOV) compared to its off-axis reflection counterpart.
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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