<scp>ddradseqtools</scp>: a software package for in silico simulation and testing of double‐digest <scp>RAD</scp>seq experiments

Mora‐Márquez, Fernando; García‐Olivares, Víctor; Emerson, Brent C.; Heredia, Unai López de

doi:10.1111/1755-0998.12550

Cited by 32 publications

(23 citation statements)

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“…We used ddRADseqTools version 0.42 (https://github.com/GGFHF/ddRADseqTools, Mora-Márquez et al ., 2017) to create in silico ddRAD digests of the A. thaliana and H. sapiens genomes. From the ddRADseqTools package, we used the script rsitesearch.py to obtain fragments from restriction sites for the commonly used EcoRI and MseI restriction enzymes within each of the reference genomes.…”

Section: Methodsmentioning

confidence: 99%

Accuracy of de novo assembly of DNA sequences from double-digest libraries varies substantially among software

LaCava

Aikens

Megna

et al. 2019

Preprint

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1Advances in DNA sequencing have made it feasible to gather genomic data for non-model 2 organisms and large sets of individuals, often using methods for sequencing subsets of the 3 genome. Several of these methods sequence DNA associated with endonuclease restriction 4 sites (various RAD and GBS methods). For use in taxa without a reference genome, these 5 methods rely on de novo assembly of fragments in the sequencing library. Many of the soft-6 ware options available for this application were originally developed for other assembly types 7 and we do not know their accuracy for reduced representation libraries. To address this im-8 portant knowledge gap, we simulated data from the Arabidopsis thaliana and Homo sapiens 9 genomes and compared de novo assemblies by six software programs that are commonly 10 used or promising for this purpose (ABySS, CD-HIT, Stacks, Stacks2, Velvet and VSEARCH). 11We simulated different mutation rates and types of mutations, and then applied the six 12 assemblers to the simulated datasets, varying assembly parameters. We found substantial 13 variation in software performance across simulations and parameter settings. ABySS failed 14 to recover any true genome fragments, and Velvet and VSEARCH performed poorly for most 15 simulations. Stacks and Stacks2 produced accurate assemblies of simulations containing 16 SNPs, but the addition of insertion and deletion mutations decreased their performance. 17CD-HIT was the only assembler that consistently recovered a high proportion of true genome 18 fragments. Here, we demonstrate the substantial difference in the accuracy of assemblies 19 from different software programs and the importance of comparing assemblies that result 20 from different parameter settings. 21

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Section: Methodsmentioning

confidence: 99%

Accuracy of de novo assembly of DNA sequences from double-digest libraries varies substantially among software

LaCava

Aikens

Megna

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…We used ddradseqtools version 0.42 (https://github.com/GGFHF/ddRADseqTools, Mora‐Márquez, García‐Olivares, Emerson, & Lo´pez de Heredia, ) to create in silico ddRAD digests of the A. thaliana and H. sapiens genomes. From the ddRADseqTools package, we used the script rsitesearch.py to obtain fragments from restriction sites for the commonly used EcoRI and MseI restriction enzymes within each of the reference genomes.…”

Section: Methodsmentioning

confidence: 99%

Accuracy of de novo assembly of DNA sequences from double‐digest libraries varies substantially among software

LaCava

Aikens

Megna

et al. 2019

Molecular Ecology Resources

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Advances in DNA sequencing have made it feasible to gather genomic data for non‐model organisms and large sets of individuals, often using methods for sequencing subsets of the genome. Several of these methods sequence DNA associated with endonuclease restriction sites (various RAD and GBS methods). For use in taxa without a reference genome, these methods rely on de novo assembly of fragments in the sequencing library. Many of the software options available for this application were originally developed for other assembly types and we do not know their accuracy for reduced representation libraries. To address this important knowledge gap, we simulated data from the Arabidopsis thaliana and Homo sapiens genomes and compared de novo assemblies by six software programs that are commonly used or promising for this purpose (ABySS, CD‐HIT, Stacks, Stacks2, Velvet and VSEARCH). We simulated different mutation rates and types of mutations, and then applied the six assemblers to the simulated data sets, varying assembly parameters. We found substantial variation in software performance across simulations and parameter settings. ABySS failed to recover any true genome fragments, and Velvet and VSEARCH performed poorly for most simulations. Stacks and Stacks2 produced accurate assemblies of simulations containing SNPs, but the addition of insertion and deletion mutations decreased their performance. CD‐HIT was the only assembler that consistently recovered a high proportion of true genome fragments. Here, we demonstrate the substantial difference in the accuracy of assemblies from different software programs and the importance of comparing assemblies that result from different parameter settings.

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“…Ejemplos de estos pipelines son Stacks (Catchen et al, 2103), Pyrad (Eaton, 2014), AftrRAD (Sovic et al, 2015), PredRAD (Herrera et al, 2015) o ddRADseqTools (Mora-Márquez et al, 2016). En general, todos los pipelines incluyen los siguientes pasos: (1) pre-procesado de las lecturas, incluyendo la evaluación de su calidad, el demultiplexado de individuos, es decir, la generación de ficheros de lecturas para cada individuo, y la eliminación de los adaptadores; (2) ensamblaje de los fragmentos secuenciados en grupos de lecturas correspondiendo cada grupo a un locus.…”

Section: Las Técnicas De Genotipado Por Secuenciación: Rad-sequnclassified

Las técnicas de secuenciación masiva en el estudio de la diversidad biológica

Heredia¹

2016

Munibe, Cienc. nat.

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ResumenLas técnicas de análisis genómico que se basan en la secuenciación masiva han supuesto una revolución en la última década no sólo en biomedicina o agronomía, sino también en el estudio de la diversidad biológica. Las plataformas de secuenciación de segunda y tercera generación que vienen a complementar a la tradicional secuenciación por el método Sanger, permiten analizar un gran número de individuos obteniendo una profundidad de secuenciación significativa de sus genomas o transcriptomas. Así, aunque todavía de manera incipiente, se vienen realizando estudios sobre la flora y fauna silvestre a escala poblacional, con especial énfasis en la determinación de patrones adaptativos frente a los cambios ambientales. En la presente revisión se describe la situación actual de las plataformas de secuenciación masiva, señalando sus ventajas y limitaciones para el análisis en organismos no modelo, para a continuación detallar las bases de dos de las técnicas más populares que se benefician de la secuenciación masiva (RAD-seq y RNA-seq) y señalar algunos ejemplos de su uso para el estudio de la diversidad biológica.Palabras clave: genoma, RAD-seq, RNA-seq, secuenciación masiva, SNP, transcriptoma. AbstractHigh-throughput sequencing based on genomic analysis techniques have not only revolutionized the fields of biomedicine or agronomy, but also the research into biological diversity. 7Secuenciación masiva y diversidad biológica Munibe, Cienc. nat. 64, 2016 • pp. 7-31 • Donostia/San Sebastián • ISSN 0214-7688 • eISSN 2172 Unai López de Heredia 1 Las técnicas de secuenciación masiva en el estudio de la diversidad biológica.Massive sequencing techniques in the study of biological diversity.

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ddradseqtools: a software package for in silico simulation and testing of double‐digest RADseq experiments

Cited by 32 publications

References 30 publications

Accuracy of de novo assembly of DNA sequences from double-digest libraries varies substantially among software

Accuracy of de novo assembly of DNA sequences from double-digest libraries varies substantially among software

Accuracy of de novo assembly of DNA sequences from double‐digest libraries varies substantially among software

Las técnicas de secuenciación masiva en el estudio de la diversidad biológica

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