What does a k-mer represent?
What does a k-mer represent?
k-mer can indicate low quality or contamination in your sequences. Usually you compute it by checking if there is a string of length k that occurs in the reads more than chance. Tools like Fastqc can also give you a visual representation to that and to what kind of sequence you see.
How do you calculate k-mer?
The fraction of a read available to contain a k-mer is (R−K+1)/R, which is the number of k-mers in the read divided by its length. That times the nucleotide coverage (C) is then the expected coverage of the k-mer.
What is a Mer in DNA?
Oligonucleotides are characterized by the sequence of nucleotide residues that make up the entire molecule. The length of the oligonucleotide is usually denoted by “-mer” (from Greek meros, “part”).
What is the best k-mer value?
Also, the best k-mer length was 61, and this should be the k-mer size when running an assembler such as Velvet, SOAPdenovo 2, ABySS, or Minia. KmerGenie outputs some great plots which show why k=61 was the choice.
What is contig in bioinformatics?
A contig (as related to genomic studies; derived from the word “contiguous”) is a set of DNA segments or sequences that overlap in a way that provides a contiguous representation of a genomic region.
What is k-mer frequency?
The frequency of a set of k-mers in a species’s genome, in a genomic region, or in a class of sequences can be used as a “signature” of the underlying sequence. Comparing these frequencies is computationally easier than sequence alignment and is an important method in alignment-free sequence analysis.
What is canonical k-mer?
A canonical k-mer is the numerical lesser of a k-mer and its reverse complement. This is useful in hashing/counting k-mers in data that is not strand specific, and thus observing k-mer is equivalent to observing its reverse complement.
What is a k-mer in biology?
In bioinformatics, k-mers are substrings of length contained within a biological sequence. Primarily used within the context of computational genomics and sequence analysis, in which k-mers are composed of nucleotides (i.e.
What is k-mer in NGS?
Usually, the term k-mer refers to all of a sequence’s subsequences of length , such that the sequence AGAT would have four monomers (A, G, A, and T), three 2-mers (AG, GA, AT), two 3-mers (AGA and GAT) and one 4-mer (AGAT). More generally, a sequence of length will have k-mers and total possible k-mers, where.
What does 10x coverage mean?
x coverage (or -fold covergae is used to describe the sequencing depth. For example, if your genome has a size of 10 Mbp and you have 100 Mbp of sequencin data that is assembled to said 10 Mbp genome, you have 10x coverage.
What is the purpose of contig?
For example, a clone contig provides a physical map of a set of cloned segments of DNA across a genomic region, while a sequence contig provides the actual DNA sequence of a genomic region.