( C) Frequency of each k-mer of u in the focal range. Our greedy algorithm selects the next node of the maximum frequency until reaching the initial node and outputs the best path (denoted by u). l = 6) in raw reads to assemble k-mers into the original tandem repeat unit. ( B) Searching the de Bruijn graph of k-mers (e.g. ( A) Select a value for k such that many short k-mers have no sequencing errors in an approximate range of a hidden tandem repeat, allowing us to reconstruct the unit string of the tandem repeat based on the de Bruijn graph approach. Published by Oxford University Press.Įstimating the unit of a hidden tandem repeat in a noisy long read. Experimental results indicated that the proposed algorithm largely outperformed Tandem Repeats Finder, a widely used program for finding tandem repeats, in terms of sensitivity.
Lilypond long repeats windows#
We exploited this characteristic to develop a method for first estimating regions that could contain a tandem repeat, by analyzing the k-mer frequency distributions of fixed-size windows across the target read, followed by an algorithm that assembles the k-mers of a putative region into the consensus repeat unit by greedily traversing a de Bruijn graph. Namely, a long tandem repeat has hundreds or thousands of approximate copies of the repeated unit, so despite the error rate, many short k-mers will be error-free in many copies of the unit. Here, we report an efficient algorithm for solving this problem that takes advantage of the length of the repeat. Moreover, most traditional algorithms for finding tandem repeats are designed to find short tandem repeats (<1000 nt) and cannot effectively handle the high error rate of long reads in a reasonable amount of time. However, new long-read sequencing technologies can produce single reads of 10 000 nt or more that can span such repeat expansions, although these long reads have high error rates, of 10-20%, which complicates the detection of repetitive elements. See An extra staff appears.Long tandem repeat expansions of more than 1000 nt have been suggested to be associated with diseases, but remain largely unexplored in individual human genomes because read lengths have been too short. Without explicitly instantiating the Voice context, extra Note: If you include relative inside a repeat Nesting \repeat volta or \repeat segno would not be. Outcome of unfolding is not the same as of writing the input musicĭiffers from the following by an octave change:Īlso, nesting \repeat unfold can be practical in ways that In some cases, especially in a \relative context, the
There are some points of interest specific to the \repeat \unfoldRepeats command, see Using repeats with MIDI. To convert the volta or segno form to the Repeats in multiple forms using the \unfoldRepeats command However, some of the examples in following sections illustrate To avoid redundancy, unfolding is not demonstrated in detail here Volta and \repeat segno commands, which are documented in The \repeat unfold command repeats music by writing it outĪ number of times.
Lilypond long repeats how to#
This section discusses how to input long (usually multi-measure)
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