Data from: Restriction site associated DNA (RAD) for de novo sequencing and marker discovery in sugarcane borer, Diatraea saccharalis Fab. (Lepidoptera: Crambidae)

Pavinato VAC, Margarido GRA, Wijeratne AJ, Wijeratne S, Meulia T, Souza AP, Michel AP, Zucchi MI

Date Published: August 1, 2016

DOI: http://dx.doi.org/10.5061/dryad.ft928

 

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Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title Final SNP set.
Downloaded 1 time
Description This file contains the final SNP set (after several filtering steps detailed at manuscript) in .vcf and .fasta format. Fasta file contains ~80bp sequences of each RADtag loci. After alignment of each sequences from same loci, SNP of each sample can be accessed.
Download final_SNP_set.zip (640.6 Kb)
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Title Minicontigs associated with RADtag loci.
Downloaded 1 time
Description Minicontigs associated with RADseq loci in .fasta format.
Download minicontigs_RADtag_loci.fa (1.777 Mb)
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Title Microsatellites found in minicontigs.
Description This file contains a table of identified microsatellite with contig ID, motif and coordinates of each motif, and a file with parameters used in MiSA for SSR search.
Download microsatellites.zip (3.494 Kb)
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Title Repetitive elements identified with RepeatMasker.
Downloaded 1 time
Description This file contains a table of the identified repetitive elements (.tbl), a file with masked contigs and repetitive elements (.fasta format) and a file with contig ID, repetitive element ID and coordinates.
Download RepeatMasker_minicontigs_RADtag_loci.zip (593.5 Kb)
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Title Blast2GO annotation file.
Downloaded 2 times
Description This .gff file contain the final annotation of minicontigs obtained using Blast2GO pipeline.
Download minicontigs_final_annotation_Blast2go.gff (612.0 Kb)
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Title Scripts and command line of each program used in this pipeline.
Downloaded 11 times
Description This file contains all necessary commands and scripts to reproduce the outputs uploaded here (SNP, minicontigs, microsatellites, repetitive element discovery and functional annotation.
Download README_Scripts_commands.txt (3.768 Kb)
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Title All kmer=27 minicontigs
Downloaded 2 times
Description This file contains minicontigs assembled with all second reads we generated. Second reads correspond to reads generated from random sheared ends of a genomic fragment. Since reads with different start and endings position were generated from the same genomic regions it allows the assemble of minicontigs bigger than read size usually sequenced (bigger than ~80bp reads)
Download all_minicontigs_random_sheared_ends_kmer27.fa (177.5 Mb)
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When using this data, please cite the original publication:

Pavinato VAC, Margarido GRA, Wijeratne AJ, Wijeratne S, Meulia T, Souza AP, Michel AP, Zucchi MI (2017) Restriction site associated DNA (RAD) for de novo sequencing and marker discovery in sugarcane borer,Diatraea saccharalisFab. (Lepidoptera: Crambidae). Molecular Ecology Resources 17(3): 454–465. http://dx.doi.org/10.1111/1755-0998.12583

Additionally, please cite the Dryad data package:

Pavinato VAC, Margarido GRA, Wijeratne AJ, Wijeratne S, Meulia T, Souza AP, Michel AP, Zucchi MI (2016) Data from: Restriction site associated DNA (RAD) for de novo sequencing and marker discovery in sugarcane borer, Diatraea saccharalis Fab. (Lepidoptera: Crambidae). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.ft928
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