A scaled-down workflow for Illumina shotgun sequencing library preparation: lower input and improved performance at small fraction of the cost
- Subject Areas
- Bioinformatics, Genomics, Molecular Biology
- next-generation sequencing, Illumina, tagmentation, sequencing library, resequencing
- © 2016 Tan et al.
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 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.2475v1
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.
This manuscript will be submitted to PeerJ for review.
Raw data for analysis
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