A scaled-down workflow for Illumina shotgun sequencing library preparation: lower input and improved performance at small fraction of the cost
Author and article information
Abstract
The high cost of library preparation remains a major obstacle to sequencing large numbers of individual genomes. Illumina’s proprietary tagmentation technology allows for rapid and easy preparation of sequencing libraries, but remains prohibitively expensive for many users. Here we propose a modified version of the protocol, which uses Illumina reagents at 1/20th the scale. We show that the scaled-down protocol performs comparably to that of the manufacturer on a non-model insect genome. Surprisingly, the scaled-down protocol also produced 14% fewer PCR duplicates that the full-scale protocol. Since PCR duplicates effectively wasted redundant data, our protocol presented here can help save not just library preparation costs, but sequencing costs as well.
Cite this as
2016. A scaled-down workflow for Illumina shotgun sequencing library preparation: lower input and improved performance at small fraction of the cost. PeerJ Preprints 4:e2475v1 https://doi.org/10.7287/peerj.preprints.2475v1Author comment
This manuscript will be submitted to PeerJ for review.
Sections
Supplemental Information
Raw data for analysis
Fields:
id: library id, starting with caste M(ales), Q(ueens) and W(orkers)
duplicates: fraction duplicated reads
method: full-scale or 1/20 total: total number of sequenced reads
mapped: percentage of mapped reads
mean: average insert size from alignment
sd: average standard deviation of insert sizes from alignment
Additional Information
Competing Interests
Alexander S Mikheyev is an Academic Editor for PeerJ.
Author Contributions
Jo Ann Tan performed the experiments, reviewed drafts of the paper.
Alexander S Mikheyev conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Data Deposition
The following information was supplied regarding data availability:
The raw data has been supplied as a supplementary file.
Funding
Funding for this research was provided by the Okinawa Institute of Science and Technology Graduate University Subsidy for Operation and JSPS KAKENHI grants 25221206 and 16H06209 to ASM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
