pblat: a multithread blat algorithm speeding up aligning sequences to genomes

Wang, Meng; Kong, Lei

doi:10.1186/s12859-019-2597-8

Cited by 78 publications

(79 citation statements)

References 11 publications

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“…2.7.0 [39] with the default parameters. The assembled transcript 23 sequences were mapped with pblat [40] to the Hi-C scaffold sequences, and the output was assessed with isoblat ver. 0.31 [41].…”

Section: Continuity Assessment With Rna-seq Read Mappingmentioning

confidence: 99%

Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?

Kadota

Nishimura

Miura

et al. 2019

Preprint

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Background: Hi-C, a derivative of chromosome conformation capture (3C) targeting the whole genome, was originally developed as a means for characterizing chromatin conformation. More recently, this method has also been frequently employed in elongating nucleotide sequences obtained by de novo genome sequencing and assembly, in which the number of resultant sequences rarely converge into the chromosome number. Despite the prevailing and irreplaceable use, sample preparation methods for Hi-C have not been intensively discussed, especially from the standpoint of genome scaffolding. Results:To gain insights into the best practice of Hi-C scaffolding, we performed a multifaceted methodological comparison using vertebrate samples and optimized various factors during sample preparation, sequencing, and computation. As a result, we have identified some key factors that help improve Hi-C scaffolding including the choice and preparation of tissues, library preparation conditions, and restriction enzyme(s), as well as the choice of scaffolding program and its usage. Conclusions:This study provides the first comparison of multiple sample preparation kits/protocols and computational programs for Hi-C scaffolding, by an academic third party. We introduce a customized protocol designated the 'inexpensive and controllable Hi-C (iconHi-C) protocol', in which the optimal conditions revealed by this study have been incorporated, and release the resultant chromosome-scale genome assembly of the Chinese softshell turtle Pelodiscus sinensis.

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Section: Continuity Assessment With Rna-seq Read Mappingmentioning

confidence: 99%

Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?

Kadota

Nishimura

Miura

et al. 2019

Preprint

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“…We generated chain files for converting coordinates from Panu_2.0 to Panu_3.0 following the protocol described at the UCSC Genome Browser (http://genomewiki.ucsc.edu/index.php/Minimal_Steps_ For_LiftOver). We split the Panu_3.0 genome into 200-kb chunks, each of which was then aligned to the Panu_2.0 genome using pblat (Wang and Kong 2019), which is the parallelized version of BLAT (Kent 2002), as described in the protocol. We used the Genome Browser utilities from http://hgdownload.cse.ucsc.edu/ admin/exe/ as described in the minimal steps protocol.…”

Section: Sequencing and Genotype Callingmentioning

confidence: 99%

Analysis of 100 high-coverage genomes from a pedigreed captive baboon colony

et al. 2019

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Baboons (genus Papio) are broadly studied in the wild and in captivity. They are widely used as a nonhuman primate model for biomedical studies, and the Southwest National Primate Research Center (SNPRC) at Texas Biomedical Research Institute has maintained a large captive baboon colony for more than 50 yr. Unlike other model organisms, however, the genomic resources for baboons are severely lacking. This has hindered the progress of studies using baboons as a model for basic biology or human disease. Here, we describe a data set of 100 high-coverage whole-genome sequences obtained from the mixed colony of olive (P. anubis) and yellow (P. cynocephalus) baboons housed at the SNPRC. These data provide a comprehensive catalog of common genetic variation in baboons, as well as a fine-scale genetic map. We show how the data can be used to learn about ancestry and admixture and to correct errors in the colony records. Finally, we investigated the consequences of inbreeding within the SNPRC colony and found clear evidence for increased rates of infant mortality and increased homozygosity of putatively deleterious alleles in inbred individuals.

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“…For annotation purposes, we relied on genomic resources available in D. melanogaster , a model species closely related to D. suzukii . More specifically we extracted from the WT3-2.0 D. suzukii genome assembly 5 kb long genomic sequences surrounding each of the 204 SNPs identified above and aligned them onto the dmel6 reference genome (Hoskins et al , 2015) using the BLAT algorithm implemented in the program pblat (Wang and Kong, 2019). The gene annotation available from the UCSC genome browser allowed us to map 169 SNPs out of the 204 SNPs onto 130 different D. melanogaster genes, 145 SNPs lying within the gene sequences and 24 less than 2.5 kb apart (our predefined threshold; Table S2).…”

Section: Resultsmentioning

confidence: 99%

A whole-genome scan for association with invasion success in the fruit flyDrosophila suzukiiusing contrasts of allele frequencies corrected for population structure

Olazcuaga

Loiseau

Parinello

et al. 2019

Preprint

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AbstractEvidence is accumulating that evolutionary changes are not only common during biological invasions but may also contribute directly to invasion success. The genomic basis of such changes is still largely unexplored. Yet, understanding the genomic response to invasion may help to predict the conditions under which invasiveness can be enhanced or suppressed. Here we characterized the genome response of the spotted wing drosophila Drosophila suzukii during the worldwide invasion of this pest insect species, by conducting a genome-wide association study to identify genes involved in adaptive processes during invasion. Genomic data from 22 population samples were analyzed to detect genetic variants associated with the status (invasive versus native) of the sampled populations based on a newly developed statistic, we called C2, that contrasts allele frequencies corrected for population structure. This new statistical framework has been implemented in an upgraded version of the program BayPass. We identified a relatively small set of single nucleotide polymorphisms (SNPs) that show a highly significant association with the invasive status of populations. In particular, two genes RhoGEF64C and cpo, the latter contributing to natural variation in several life-history traits (including diapause) in Drosophila melanogaster, contained SNPs significantly associated with the invasive status in the two separate main invasion routes of D. suzukii. Our methodological approaches can be applied to any other invasive species, and more generally to any evolutionary model for species characterized by non-equilibrium demographic conditions for which binary covariables of interest can be defined at the population level.

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pblat: a multithread blat algorithm speeding up aligning sequences to genomes

Cited by 78 publications

References 11 publications

Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?

Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?

Analysis of 100 high-coverage genomes from a pedigreed captive baboon colony

A whole-genome scan for association with invasion success in the fruit flyDrosophila suzukiiusing contrasts of allele frequencies corrected for population structure

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