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The competition has begun! We're giving away a $50 Amazon gift card to the member who answers the most questions on our site during the month. We want to encourage our community members to share their knowledge and help each other out by answering questions related to sequencing technologies, genomics, and bioinformatics. The competition is open to all members of the site, and the winner will be announced at the beginning of July. Best of luck!

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  • ychang
    replied
    if you want whole genome resequencing, I can help!
    All-in-one sequencing: an improved library preparation method for cost-effective and high-throughput next-generation sequencing - Plant Methods
    https://plantmethods.biomedcentral.com/articles/10.1186/s13007-020-00615-3
    Background Next generation sequencing (NGS) has been widely used in biological research, due to its rapid decrease in cost and increasing ability to generate data. However, while the sequence generation step has seen many improvements over time, the library preparation step has not, resulting in low-efficiency library preparation methods, especially for the most time-consuming and labor-intensive steps: size-selection and quantification. Consequently, there can be bottlenecks in projects with large sample cohorts. Results We have described the all-in-one sequencing (AIO-seq) method, where instead of performing size-selection and quantification for samples individually, one sample one tube, up to 116 samples are pooled and analyzed in a single tube, ‘All-In-One’. The AIO-seq method pools libraries based on the samples’ expected data yields and the calculated concentrations of the size selected regions (target region), which can easily be obtained with the Agilent 2100 Bioanalyzer and Qubit Fluorometer. AIO-seq was applied to whole genome sequencing and RNA-seq libraries successfully, and it is envisaged that it could be applied to any type of NGS library, such as chromatin immunoprecipitation coupled with massively parallel sequencing, assays for transposase-accessible chromatin with high-throughput sequencing, and high-throughput chromosome conformation capture. We also demonstrated that for genetic population samples with low coverage sequences, like recombinant inbred lines (RIL), AIO-seq could be further simplified, by mixing the libraries immediately after PCR, without calculating the target region concentrations. Conclusions The AIO-seq method is thus labor saving and cost effective, and suitable for projects with large sample cohorts, like those used in plant breeding or population genetics research.

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  • yannickwurm
    started a topic Cheaper library prep service provider?

    Cheaper library prep service provider?

    Hello,
    there are multiple published manners of getting much cheaper library preparations if you do them in-house. That's great if you have a qualified tech who has trained to do this on staff or time/skills to do it yourself. However for some of us that's not the case!

    Are there any service providers that will do RNAseq preps at e.g. 1/10th volume or using one of the other published tricks? Library prep costs are still a killer for many projects....

    Thanks!
    Yannick
    Tags: dna, illumina, library preparation, rnaseq, service provider
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