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But even if it is satire, it is a failure in that regard, as ultimately one should be able to tell at the end of the read.
A richer assumption is that errors are more likely towards the end of the read, but are otherwise random as to base and location.
Analysis of D3 (another 1000 genomes dataset) revealed another striking anomaly in base call frequencies, shown in Figure S3, with base frequency varying wildly with position and significant falloff in calling of A towards the end of the read.
The bias towards the reference allele with local alignments has been described before [25] and results from soft masking (i.e.: ignoring) the end of the read if a mismatch between reference and read is observed.
Whilst this sequence is at the end of the read and therefore the quality is less assured, these supplemental amino acids are also present in the HSPs of other crustaceans.
Pyrosequencing error rates increase toward the end of the read, but we assume it is possible to trim the reads to confine the error rate to an acceptable level.
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Figure 2 has strong similarity to a graph presented by Dohm et al. [10], showing a fall in quality scores toward the end of the reads.
The general principle to label the reads spanning the linked contigs is to use 'fmX' to represent the 5' end of the reads located in contigX and 'toY' to represent the 3' end of the reads located in contigY.
First, all bases at the 3' end of the reads with quality scores of 3 or lower were removed.
Because the quality of Illumina reads decreases toward the end of the reads, PANDAseq will therefore incorrectly merge reads that do not overlap.
BS-Seeker2 circumvents these problems by using local alignments to remove the mismatched nucleotides from the end of the reads to maximize the mappability.
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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