Custom

Glad you asked! When you are ready to proceed, please submit the Custom Project Intake Form. If you need extra help planning out your sequencing assay before getting started, please email support@plasmidsaurus.com for assistance.

The cost for each Custom Sequencing project starts at $500 for the 1st Gb (gigabase) of total raw data, then adds $50 for each additional 1 Gb. If barcodes are required for multiplexing, this adds a $50 charge per sample:

Project Cost = $500 base price for 1st Gb data + $50 for each extra Gb data + $50 x number of samples

We calculate your project price when you submit the Custom Project Intake Form. Note that each batch of shipped samples starts again at the base price of $500, so if you are prioritizing cost over speed, please consider reducing the number of batches you ship us to minimize your overall project price. 

In the vast majority of cases, we deliver Custom Sequencing results within 3-5 business days of receipt of your samples at the Eugene, Oregon lab. Projects that require very large amounts of data, or add on extra services such as DNA extraction or bioinformatics, may take longer.

In most cases, we deliver only the raw sequencing reads (in .fastq format) for Custom projects. Any analyses (demultiplexing internal barcodes, generating consensus sequences, binning or aligning variants, etc.) must be done by the researcher, unless we specifically agree to perform analysis during project setup.

Due to variation in sample quality and other stochastic factors, the samples within a project may produce slightly different amounts of data. Any sample in the project that produces at least 75% of its data target will be denoted “complete” in your results and is not eligible for free rerun.

Any sample that produces less than 75% of its data target will be denoted “fail” in your results and will be automatically resequenced at no additional charge in an attempt to collect more data. If the sequencing performance on the initial run is particularly poor, we may also ask you to ship us a replacement sample for the rerun.

Note: If your project requires that all samples achieve a minimum data target (i.e. you cannot accept any samples that produce only 75% of the average data target), please let us know during project set-up and we will increase the data target such that obtaining 75% of the average target would still meet your minimum requirement. You will be charged according to this increased target.

We construct an Oxford Nanopore amplification-free long-read sequencing library using the newest v14 library prep chemistry.

• For circular dsDNA, we use tagmentation to linearize each molecule in a sequence-independent manner.
• For linear dsDNA, we use sequence-independent end-ligation.
• For genomic dsDNA, we use sequence-independent tagmentation that minimally fragments the gDNA (unless you specifically request that we switch to end-ligation instead).

We then sequence the library with a primer-free protocol using the most accurate R10.4.1 flow cells to collect the amount of data that you specifically request. Please do not ship any primers with or mixed into your samples.

You will receive only the raw sequencing reads (in .fastq format) for Custom Sequencing projects, unless we specifically agree to perform an analysis during project set-up.

We require a minimum raw read Qscore of 10 (90% accuracy) during sequencing, although most raw reads are above Q20 (99% accuracy). We use the super-accurate basecalling model.

Since we typically do not perform any further analysis of the raw reads for Custom Sequencing, the final accuracy of your own analysis will depend on your analysis pipeline and quality filtering.

For variant libraries
Total Data Required = Number of samples x Insert length x Number of variants (barcodes, mutants, etc.) x Coverage required per variant

For genomic sequencing
Total Data Required = Number of samples x Expected genome size x Coverage required per genome

We fluorometrically quantify your input DNA and multiplex the samples in equimolar ratio for sequencing. Due to variation in sample quality and other stochastic factors, the samples may still produce slightly different amounts of data. Every custom project does include a free increase to the project data target to account for some expected variability, but lower quality samples may still fail to achieve the target. Therefore, the data target should be interpreted as an average per-sample target of basecalled data, where some samples may end up higher and others may end up lower.

If you need different amounts of data for each sample, you can request this! Just let us know when you set up your order. 

In most cases, we deliver only the raw sequencing reads (in .fastq format) for Custom projects. Any analyses (demultiplexing internal barcodes, generating consensus sequences, binning or aligning variants, etc.) must be done by the researcher, unless we specifically agree to perform analysis during project setup.

We do not accept RNA for Custom Sequencing at this time, so you would need to convert your RNA into double-stranded cDNA before shipping it to us.

Single-stranded DNA is not currently a supported application for Custom Sequencing, but we do have some beta methods in development that we might be able to test out. Please email support@plasmidsaurus.com to inquire about ssDNA sequencing options.

Yes! We perform do a wide range of special workflows, such as delivering POD5 files or methylation BAM files, Adaptive Sampling to enrich or deplete a sequence of interest, read filtering to retain only specific lengths, or swapping out ONT long-read data for Illumina short-read data. If you're interested in any of these or any other special workflows, please explain the nature of your special request when you submit the Custom Project Intake Form. Note that some types of requests may incur an additional fee.