Tandem Repeat Long Reads

In this paper we present mixtar the first de novo method for tandem repeat detection that combines the high quality of short reads and the large length of long reads. Tandem dna repeats can be sequenced with long read technologies but cannot be accurately deciphered due to the lack of computational tools taking high error rates of these technologies into account. For many trs however these features are very difficult if not impossible to assess requiring low throughput and labor intensive assays.

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Long terminal repeat long terminal repeats ltrs are identical sequences of dna that repeat hundreds or thousands of times found at either end of retrotransposons or proviral dna formed by reverse transcription of retroviral rna.

Tandem repeat long reads. Tandem repeats trs can cause disease through their length sequence motif interruptions and nucleotide modifications. A single read that spans over the tandem repeat reveals the repeat cluster to be of length 12 2k which suggests that the flye length estimate is more accurate. These methods align the reads to a reference genome then get the reads that cover a tandem repeat region of the reference and perform sophisticated probability based comparisons of these reads to the sequence of the repeating unit. They are used by viruses to insert their genetic material into the host genomes.

Tidehunter is an efficient and sensitive tandem repeat detection and consensus calling tool which is designed for tandemly repeated long read sequence inc seq r2c2 nanoampli seq. Using long read sequence data from apes and humans we present a sequence based evolutionary framework for 20 000 phased strs and vntrs. Our hybrid algorithm uses the set of short reads for tandem repeat pattern detection based on a de bruijn graph. Tandem repeat expansions are responsible for a growing list of human diseases even though it is hard to determine tandem repeat sequences with current dna sequencing technology.

Recent long read technologies are promising because the dna reads are often longer than the repetitive regions but are hampered by high error rates. Short tandem repeats strs and variable number tandem repeats vntrs are among the most mutable regions of our genome but are frequently underascertained in studies of disease and evolution. The initial run takes in an alignment file alignment of long reads with the reference such as hg19 and a reference tandem repeat table as input and generates an output file with estimated tanderm repeat region in the long read expected value of the number of tandem repeat elements estimated structural variation region in the tandem repeat. We are aware of two previous methods for determining tandem repeat copy number from long dna reads.

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