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For quality assurance purposes, each reader examined a blinded panel of 30 slides each by ZN and by LED FM (10 slides by each method) prior to the start of reading smears from clinical specimens.
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The divergence at the start of reads however remains present.
Unusual behaviour is found at the start of reads, where the selected k-mers have unusually high or low frequencies (see Figure 3).
For example, the base A is significantly overrepresented at the start of reads, while k-mers such as poly-T are dramatically underrepresented; the k-mers in the middle few bases of the reads are distributed differently to the other k-mers.
For each demultiplexed sample, we computationally sorted reads based on their locus of origin and reaction type (E or G) by matching the start of read 1 to each of the 60 3' flank primers and the start of read 2 to each of the 60 5' flank primers (E reactions) or the L1-specific primer (G reactions) (Additional file 3: Figure S2).
If edges e and e′ represent consecutive regions in the genome, then the genomic distance from the start of read r to the start of read r′ equals to L e n g t h (e ) − x 0 + y 0, where Length e) stands for the length of edge e.
We further removed the first 10 and last 11 bp of the reads, since the start of reads showed a different nucleotide composition compared to the rest of the sequence and the end of reads showed a decrease in quality (data not shown).
At a certain point in our lives something terrific happens — the stops and starts of reading begin to flow and we are able to turn our complete attention to the text itself.
Thus use of our techniques can give insight into these biases in read starting positions: analysing the over- and under-represented sequences at the starts of reads by calculating p-values as described in Section "Analysing occurrences of k-mers" might indicate favoured and avoided positions in a genome on a sequence level.
From the start, this business of reading friends' books was uneasy-making.
Most of these putative Dicer-processed tRNAs, including eight cases reported to generate products with miRNA-like features in literature, exhibit read blocks distinguished by precise start position of reads.
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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