Data from: Identifying conserved genomic elements and designing universal bait sets to enrich them

Faircloth BC

Date Published: November 13, 2017

DOI: https://doi.org/10.5061/dryad.v0k4h

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Title Arachnida Bait Design and Testing Files
Downloaded 2 times
Description The ZIP archive contains the files used to identify, design, and test probes targeting conserved loci in Arachnids. The *-design-steps.md file is a description of the design steps followed for the group. The "BAM" directory contains mappings of real/simulated reads to the base genome sequence for the group. The "BED" directory contains BAM files converted to BED, as well as intermediate BED files created during BED processing. The "BED" directory also contains the database of putatively conserved loci in the exemplar+base genome taxa, and the temporary probe design file. The "*-probes" directory contains the database of temporary probe mappings to exemplar taxa, several intermediate files, and the principal probe design file. The "in-silico-test" directory contains all data from in-silico testing of the principal probe design file.
Download arachnida.zip (694.7 Mb)
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Title Arachnida-UCE-1.1K-v1 Bait Design
Downloaded 1 time
Description A target enrichment probe set designed from 1,120 UCE loci identified among arachnids. This is a ZIP archive of a FASTA file that is ready for submission of the probe set for synthesis.
Download Arachnida-UCE-1.1K-v1.fasta.zip (777.2 Kb)
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Title Coleoptera Bait Design and Testing Files
Downloaded 2 times
Description The ZIP archive contains the files used to identify, design, and test probes targeting conserved loci in Coleoptera. The *-design-steps.md file is a description of the design steps followed for the group. The "BAM" directory contains mappings of real/simulated reads to the base genome sequence for the group. The "BED" directory contains BAM files converted to BED, as well as intermediate BED files created during BED processing. The "BED" directory also contains the database of putatively conserved loci in the exemplar+base genome taxa, and the temporary probe design file. The "*-probes" directory contains the database of temporary probe mappings to exemplar taxa, several intermediate files, and the principal probe design file. The "in-silico-test" directory contains all data from in-silico testing of the principal probe design file.
Download coleoptera.zip (82.04 Mb)
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Title Coleoptera-UCE-1.1K-v1 Bait Design
Downloaded 2 times
Description A target enrichment probe set designed from 1,172 UCE loci identified among Coleoptera. This is a ZIP archive of a FASTA file that is ready for submission of the probe set for synthesis.
Download Coleoptera-UCE-1.1K-v1.fasta.zip (702.9 Kb)
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Title Diptera Bait Design and Testing Files
Downloaded 2 times
Description The ZIP archive contains the files used to identify, design, and test probes targeting conserved loci in Diptera. The *-design-steps.md file is a description of the design steps followed for the group. The "BAM" directory contains mappings of real/simulated reads to the base genome sequence for the group. The "BED" directory contains BAM files converted to BED, as well as intermediate BED files created during BED processing. The "BED" directory also contains the database of putatively conserved loci in the exemplar+base genome taxa, and the temporary probe design file. The "*-probes" directory contains the database of temporary probe mappings to exemplar taxa, several intermediate files, and the principal probe design file. The "in-silico-test" directory contains all data from in-silico testing of the principal probe design file.
Download diptera.zip (500.6 Mb)
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Title Diptera-UCE-2.7K-v1 Bait Design
Downloaded 1 time
Description A target enrichment probe set designed from 2,711 UCE loci identified among Diptera. This is a ZIP archive of a FASTA file that is ready for submission of the probe set for synthesis.
Download Diptera-UCE-2.7K-v1.fasta.zip (1.654 Mb)
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Title Hemiptera Bait Design and Testing Files
Downloaded 2 times
Description The ZIP archive contains the files used to identify, design, and test probes targeting conserved loci in Hemiptera. The *-design-steps.md file is a description of the design steps followed for the group. The "BAM" directory contains mappings of real/simulated reads to the base genome sequence for the group. The "BED" directory contains BAM files converted to BED, as well as intermediate BED files created during BED processing. The "BED" directory also contains the database of putatively conserved loci in the exemplar+base genome taxa, and the temporary probe design file. The "*-probes" directory contains the database of temporary probe mappings to exemplar taxa, several intermediate files, and the principal probe design file. The "in-silico-test" directory contains all data from in-silico testing of the principal probe design file.
Download hemiptera.zip (226.4 Mb)
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Title Hemiptera-UCE-2.7K-v1 Bait Design
Description A target enrichment probe set designed from 2,731 UCE loci identified among Hemiptera. This is a ZIP archive of a FASTA file that is ready for submission of the probe set for synthesis.
Download Hemiptera-UCE-2.7K-v1.fasta.zip (2.125 Mb)
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Title Lepidoptera Bait Design and Testing Files
Downloaded 2 times
Description The ZIP archive contains the files used to identify, design, and test probes targeting conserved loci in Lepidoptera. The *-design-steps.md file is a description of the design steps followed for the group. The "BAM" directory contains mappings of real/simulated reads to the base genome sequence for the group. The "BED" directory contains BAM files converted to BED, as well as intermediate BED files created during BED processing. The "BED" directory also contains the database of putatively conserved loci in the exemplar+base genome taxa, and the temporary probe design file. The "*-probes" directory contains the database of temporary probe mappings to exemplar taxa, several intermediate files, and the principal probe design file. The "in-silico-test" directory contains all data from in-silico testing of the principal probe design file.
Download lepidoptera.zip (240.2 Mb)
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Title Lepidoptera-UCE-1.3K-v1 Bait Design
Downloaded 1 time
Description A target enrichment probe set designed from 1,381 UCE loci identified among Lepidoptera. This is a ZIP archive of a FASTA file that is ready for submission of the probe set for synthesis.
Download Lepidoptera-UCE-1.3K-v1.fasta.zip (722.4 Kb)
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When using this data, please cite the original publication:

Faircloth BC (2017) Identifying conserved genomic elements and designing universal bait sets to enrich them. Methods in Ecology and Evolution 8(9): 1103-1112. https://doi.org/10.1111/2041-210x.12754

Additionally, please cite the Dryad data package:

Faircloth BC (2017) Data from: Identifying conserved genomic elements and designing universal bait sets to enrich them. Dryad Digital Repository. https://doi.org/10.5061/dryad.v0k4h
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