The escape sequence
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Unfortunately, homopolymers are a source of errors in sequencing, particularly for long-read technologies. While substitutions seem to be randomly distributed along the reads for PacBio and ONT, the main error mode seems to be indels in homopolymeric sections, i.e. reading the same nucleotide several times or skipping over one of the repeated nucleotides. Many studies show that homopolymeric indels are the main type of error for PacBIO SMRT and ONT long-read sequencing68,99–101. This is even the case for PacBio HiFi reads, while the circular consensus approach eliminates the randomly distributed substitutions but homopolymer indels remain87. It seems that ONT reads are more prone to this type of error than PacBIo56. The rate of these errors is independent of the length of the homopolymer for ONT, but it rises with homopolymer length for short-read and PacBio technologies102.
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