Author: Jakub M Bartoszewicz; Anja Seidel; Bernhard Y Renard
Title: Interpretable detection of novel human viruses from genome sequencing data Document date: 2020_1_30
ID: ac00tai9_31
Snippet: We use an all-zero reference. As reads from real sequencing runs are usually not equally long, shorter reads must be padded with N s; the "unknown" nucleotide is also called whenever there is not enough evidence to assign any other to the raw sequencing signal. Therefore, N s are "null" nucleotides and are a natural candidate for the reference input. We do not consider alternative solutions based on GC content or dinucleotide shuffling, as the in.....
Document: We use an all-zero reference. As reads from real sequencing runs are usually not equally long, shorter reads must be padded with N s; the "unknown" nucleotide is also called whenever there is not enough evidence to assign any other to the raw sequencing signal. Therefore, N s are "null" nucleotides and are a natural candidate for the reference input. We do not consider alternative solutions based on GC content or dinucleotide shuffling, as the input reads originate from multiple different species, and the sequence composition may itself be a strong marker of both virus and host taxonomy.
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