Data from: The effects of read length, quality and quantity on microsatellite discovery and primer development: from Illumina to PacBio

Wei N, Bemmels JB, Dick CW

Date Published: February 25, 2014

DOI: http://dx.doi.org/10.5061/dryad.r20t0

 

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Title Read length simulations without sequencing errors
Downloaded 36 times
Description Sequences of uniform length at each of 100, 150, 200, 250, 300, 350, 400, 500, 600, 700, 800, 1000 and 1200 bp were drawn at random from Populus trichocarpa chromosomes 1–19 (v3.0, DOE-JGI, http://www.phytozome.net/poplar) using 0.1x coverage. Simulations were conducted using Grinder v0.5.3 without the inclusion of sequencing errors.
Download ReadLengthSim_noErrors.zip (204.5 Mb)
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Title Read length simulations with sequencing errors
Downloaded 38 times
Description Sequences of uniform length at each of 100, 150, 200, 250, 300, 350, 400, 500, 600, 700, 800, 1000 and 1200 bp were drawn at random from Populus trichocarpa chromosomes 1–19 (v3.0, DOE-JGI, http://www.phytozome.net/poplar) using 0.1x coverage. Simulations were conducted using PBSIM v1.0.3 with built-in PacBio CCS error profiles (substitutions/insertions/deletions ratio of 6:21:73; read accuracy of 98 ± 2%).
Download ReadLengthSim_withErrors.zip (154.0 Mb)
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Title Sequencing error simulations
Downloaded 36 times
Description Sequencing errors of substitutions and indels (insertions and deletions) were introduced to reads of uniformly 350 bp simulated from Populus trichocarpa chromosomes 1–19 (v3.0, DOE-JGI, http://www.phytozome.net/poplar) at 0.1x coverage using Grinder v0.5.3. In terms of sequencing error type, simulations included substitution-biased (substitutions/indels ratio of 90:10) and indel-biased (substitutions/indels ratio of 10:90) sequencing errors. In terms of sequencing error rate distribution, we assumed that sequencing errors occurred either uniformly or linearly from the 5′ end to 3′ end of each read. With uniformly distributed sequencing errors, reads were simulated with an error rate of 0, 0.01%, 0.1%, 0.5%, 1%, 2%, 3%, and 5%. With linearly distributed errors, the error rate doubled from the 5′ end to 3′ end: 0, 0.01–0.02%, 0.1–0.2%, 0.2–0.4%, 0.5–1%, 1–2%, and 2–4%. For the file name of each simulation, the first three letters reflect the error rate distribution (e.g. Lin for linear error rate distribution, Uni for uniform distribution); the following 4 digits represent the sequencing error type (e.g. 9010 for substitutions/indels ratio of 90:10); the remaining digits indicate the error rate (e.g. 0.1%). When error rate was 0, the simulation was designated as ErrorRate_0.
Download SeqErrorSim.zip (433.3 Mb)
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Title Error trimming simulation
Downloaded 13 times
Description Sequences of uniform length of 350 bp were drawn at random from Populus trichocarpa chromosomes 1–19 (v3.0, DOE-JGI, http://www.phytozome.net/poplar) at 0.1x coverage using PBSIM v1.0.3, following the observed read length distribution and quality profiles of Triplaris cumingiana CCS reads in this study.
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When using this data, please cite the original publication:

Wei N, Bemmels JB, Dick CW (2014) The effects of read length, quality and quantity on microsatellite discovery and primer development: from Illumina to PacBio. Molecular Ecology Resources 14(5): 953-965. http://dx.doi.org/10.1111/1755-0998.12245

Additionally, please cite the Dryad data package:

Wei N, Bemmels JB, Dick CW (2014) Data from: The effects of read length, quality and quantity on microsatellite discovery and primer development: from Illumina to PacBio. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.r20t0
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