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High sensitivity and specificity, using base qualities at all steps in the alignment. Includes adapter trimming, base quality calibration, Bi-Seq alignment, and options for reporting multiple alignments per read. Use of ambiguous IUPAC codes in reference for common SNPs can improve SNP recall and remove allelic bias. Yes Yes Yes
BBDuk multithreaded tool to trim adapters and filter or mask contaminants based on kmer-matching, allowing a hamming- or edit-distance, as well as degenerate bases. Also performs optimal quality-trimming and filtering, format conversion, contaminant concentration reporting, gc-filtering, length-filtering, entropy-filtering, chastity-filtering ...
For example, the built-in reverse complement utility reverses the order of characters and replaces each with its complement. [17] The screenshots demonstrate the use of MEGA's reverse complement tool. The original sequence was reversed and each nucleotide was replaced with its complement to produce the reverse complement.
(In each strand, tag α is the reverse complement of tag β and vice versa). The libraries containing duplex tags and Illumina adapters are sequenced using the Illumina TruSeq system. Reads that are originating from every single strand of DNA form a group of reads (tag families) that share the same tag.
A single tree can capture up to 250 tons in its lifetime, the equivalent of removing nearly 200 cars from the road for an entire year. But between logging and fires, 95% of California's redwoods ...
A young North Carolina woman was doused in gasoline and set on fire by a sick suspect who then fled — leaving her heartbroken mother wondering, “How could they do this to my baby?”
Degenerate base symbols in biochemistry are an IUPAC [2] [3] representation for a position on a DNA sequence that can have multiple possible alternatives. These should not be confused with non-canonical bases because each particular sequence will have in fact one of the regular bases.
Trump will probably make a show of eviscerating Biden’s climate plans while rebranding some of them as his own. Markets, in the end, may move in more or less the same direction.