Noise-Cancelling Repeat Finder: Uncovering tandem repeats in error-prone long-read sequencing data

Harris, Robert S.; Čechová, Monika; Makova, Kateryna D.

doi:10.1101/475194

Cited by 3 publications

(3 citation statements)

References 21 publications

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“…In total, five error rates with different substitution: insertion: deletion ratios (13%, 41:23:36, 15%-a, 37:42:21, 15%-b, 11:60:29, 16%, 28:24:48 and 20%, 48:15:37), five repeat pattern sizes (100, 500, 1000, 2000 and 3000) and five copy numbers (2, 3, 5, 10 and 20) were used to generate 15 simulated datasets (Tables 1–3). The five error rates and error distributions come from five public real datasets (PacBio: 15%-a, 15%-b and ONT: 13%, 16%, 20%) (Weirather et al , 2017; Harris et al , 2018). For each simulated dataset, 1000 reads were generated.…”

Section: Resultsmentioning

confidence: 99%

TideHunter: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain

et al. 2019

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Motivation Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) sequencing technologies can produce long-reads up to tens of kilobases, but with high error rates. In order to reduce sequencing error, Rolling Circle Amplification (RCA) has been used to improve library preparation by amplifying circularized template molecules. Linear products of the RCA contain multiple tandem copies of the template molecule. By integrating additional in silico processing steps, these tandem sequences can be collapsed into a consensus sequence with a higher accuracy than the original raw reads. Existing pipelines using alignment-based methods to discover the tandem repeat patterns from the long-reads are either inefficient or lack sensitivity. Results We present a novel tandem repeat detection and consensus calling tool, TideHunter, to efficiently discover tandem repeat patterns and generate high-quality consensus sequences from amplified tandemly repeated long-read sequencing data. TideHunter works with noisy long-reads (PacBio and ONT) at error rates of up to 20% and does not have any limitation of the maximal repeat pattern size. We benchmarked TideHunter using simulated and real datasets with varying error rates and repeat pattern sizes. TideHunter is tens of times faster than state-of-the-art methods and has a higher sensitivity and accuracy. Availability and implementation TideHunter is written in C, it is open source and is available at https://github.com/yangao07/TideHunter

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Section: Resultsmentioning

confidence: 99%

TideHunter: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain

et al. 2019

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“…2) The pipelines used to annotate the repeats were not able to identify the satellite DNA arrays. According to [46], computational tools that take into account the high error rates of long-read technologies are lacking [46]. The employment of personalized pipelines, such as in [6] [47] [48], or tools specifically designed for satellite analysis in long-reads, like NCRF [46], tandem-genotypes [49], P ACMON STR [50], TandemTools [51] and Winnowmap2 [52], could improve the satellite DNA annotation results.…”

Section: Satellite Dnamentioning

confidence: 99%

De novo assembly and characterization of a highly degenerated ZW sex chromosome in the fish Megaleporinus macrocephalus

Borges,

Utsunomia,

Varani

et al. 2024

Preprint

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Background: Megaleporinus macrocephalus (piaucu) is a Neotropical fish within Characoidei that presents a well-established heteromorphic ZZ/ZW sex-determination system and thus, constitutes a good model for studying W and Z chromosomes in fishes. We used PacBio reads and Hi-C to assemble a chromosome-level reference genome for M. macrocephalus. We generated family segregation information to construct a genetic map, pool-seq of males and females to characterize its sex system, and RNA-seq to highlight candidate genes of M. macrocephalus sex determination. Results: M. macrocephalus reference genome is 1,282,030,339 bp in length and has a contig and scaffold N50 of 5.0 Mb and 45.03 Mb, respectively. Based on patterns of recombination suppression, coverage, Fst, and sex-specific SNPs, three major regions were distinguished in the sex chromosome: W-specific (highly differentiated), Z-specific (in degeneration), and PAR. The sex chromosome gene repertoire was composed of genes from the TGF-beta family (amhr2, bmp7) and Wnt/beta-catenin pathway (wnt4, wnt7a), and some of them were differentially expressed. Conclusions: The chromosome-level genome of piaucu exhibits high quality, establishing a valuable resource for advancing research within the group. Our discoveries offer insights into the evolutionary dynamics of Z and W sex chromosomes in fish, emphasizing ongoing degenerative processes and indicating complex interactions between Z and W sequences in specific genomic regions. Notably, amhr2 and bmp7 are potential candidate genes for sex determination in M. macrocephalus.

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“…The combination of cytogenetics and genomics studies has proven to be useful in elucidating numerous aspects of genome evolution and organization [30,31], with particular emphasis on repetitive DNAs [6,[32][33][34]. Furthermore, due to their tandemly repeated genomic organization, satDNA studies in non-model organisms were boosted in the last few years, especially with the development of several assembly-free pipelines designed for using raw reads [35][36][37][38]. In this context, several satDNA catalogs were characterized in a variety of invertebrate and vertebrate species [6,34,[39][40][41][42][43][44].…”

Section: Introductionmentioning

confidence: 99%

Evolution of ancient satellite DNAs in extant alligators and caimans (Crocodylia, Reptilia)

Sales-Oliveira,

dos Santos,

Goes

et al. 2024

BMC Biol

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Background Crocodilians are one of the oldest extant vertebrate lineages, exhibiting a combination of evolutionary success and morphological resilience that has persisted throughout the history of life on Earth. This ability to endure over such a long geological time span is of great evolutionary importance. Here, we have utilized the combination of genomic and chromosomal data to identify and compare the full catalogs of satellite DNA families (satDNAs, i.e., the satellitomes) of 5 out of the 8 extant Alligatoridae species. As crocodilian genomes reveal ancestral patterns of evolution, by employing this multispecies data collection, we can investigate and assess how satDNA families evolve over time. Results Alligators and caimans displayed a small number of satDNA families, ranging from 3 to 13 satDNAs in A. sinensis and C. latirostris, respectively. Together with little variation both within and between species it highlighted long-term conservation of satDNA elements throughout evolution. Furthermore, we traced the origin of the ancestral forms of all satDNAs belonging to the common ancestor of Caimaninae and Alligatorinae. Fluorescence in situ experiments showed distinct hybridization patterns for identical orthologous satDNAs, indicating their dynamic genomic placement. Conclusions Alligators and caimans possess one of the smallest satDNA libraries ever reported, comprising only four sets of satDNAs that are shared by all species. Besides, our findings indicated limited intraspecific variation in satellite DNA, suggesting that the majority of new satellite sequences likely evolved from pre-existing ones.

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Noise-Cancelling Repeat Finder: Uncovering tandem repeats in error-prone long-read sequencing data

Cited by 3 publications

References 21 publications

TideHunter: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain

TideHunter: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain

De novo assembly and characterization of a highly degenerated ZW sex chromosome in the fish Megaleporinus macrocephalus

Evolution of ancient satellite DNAs in extant alligators and caimans (Crocodylia, Reptilia)

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