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Fig. 1 | Genome Biology

Fig. 1

From: STRling: a k-mer counting approach that detects short tandem repeat expansions at known and novel loci

Fig. 1

STRling uses several types of read evidence to infer STR location and size. A STRling performs k-mer counting in reads that are soft-clipped, unaligned, or aligned to a large STR in the reference genome. For each k-mer of length 2–6 bp, STRling selects the one that covers the largest proportion of the read. If two are equal, the smallest is chosen. B Where a pair of reads has one read that maps well to the reference genome, and a mate with high STR content, the mapping position of the well-mapped read is used to reposition the STR read. These “anchored pairs” aid in refining the location and improve the quantification of sequence support for the putative STR. C Different classes of reads are used to support STR alleles of varying length. Small alleles, shorter than the read length, can be detected by spanning reads, and typically have many spanning pairs. Medium expansions, of a length between the read length and the fragment size, are indicated by anchored pairs and few spanning pairs. Soft-clipped reads can be used to infer the precise insertion point. Large expansions, those longer than the fragment size, are evidenced by a larger number of anchored pairs, as well as contributing unplaced pairs

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