TRA: Tandem repeat assembler for next generation sequences
Version 2 2024-06-03, 12:10Version 2 2024-06-03, 12:10
Version 1 2017-03-28, 21:18Version 1 2017-03-28, 21:18
conference contribution
posted on 2024-06-03, 12:10 authored by Y Jiang, J Lu, Jingyu HouJingyu Hou, W Zhou© 2017 ACM. Eukaryotic genomes contain high volumes of intronic and intergenic regions in which repetitive sequences are abundant. These repetitive sequences represent challenges in genomic assignment of short read sequences generated through next generation sequencing and are often excluded in analysis losing invaluable genomic information. Here we present a method, known as TRA (Tandem Repeat Assembler), for the assembly of repetitive sequences by constructing contigs directly from paired-end reads. Using an experimentally acquired data set for human chromosome 14, tandem repeats >200 bp were assembled. Alignment of the contigs to the human genome reference (GRCh38) revealed that 84.3% of tandem repetitive regions were correctly covered. For tandem repeats, this method outperformed state-of-the-art assemblers by generating correct N50 of contigs up to 512 bp.
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1-6Location
Geelong, VictoriaPublisher DOI
Start date
2017-01-30End date
2017-02-03ISBN-13
9781450347686Language
engPublication classification
E Conference publication, E1 Full written paper - refereedCopyright notice
2017, ACMTitle of proceedings
ACSW '17 Proceedings of the Australasian Computer Science Week MulticonferenceEvent
Australasian Computer Science Week. Multiconference (2017 : Geelng, Victoria)Publisher
ACMPlace of publication
New York, N.Y.Usage metrics
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