Project Planner

How to use Project Planner:

The Input tab is designed to for you customize your samples, settings for specific applications, and optionally change the default settings for applications.

  1. Sample Input table

    • Click the update button on the right (alternatively delete/add rows)
    • Update the sample/group name
    • Update the genome size (Gbp) & expected ploidy
    • Update the quantity of samples included in this experiment
    • Select your applications of interest

  2. Applications Settings table

    • Some applications require additional information (e.g., how many cells do you want to target for scRNA?). Only edit this table if necessary.

  3. Sequencing Depth table

    • Editing this table is optional
    • We have set default recommended values for sequencing depth or number of reads for each application and technology. For example, if you are interested in genome assembly, you will need much higher coverage with short-read technologies to achieve optimal performance compared to using high-accuracy long-read technologies. However, optionally, you can edit the Sequencing Depth table for each application and technology.

  4. Navigate to the Output tab

Sample Input

Other Application Settings

Sequencing Depth

Instruments

The Instruments tab provides a summary of current/supported technologies, sequencing instruments, and flow cells including number of cells that can be run simultaneously, run time, average data quality, read lengths, yield (Gbp), reads (millions), cost-per-flowcell, cost-per-Gbp, and instrument cost. Rows are colored by sequencing technology.

By default, we hide lower-throughput platforms for simplicity. However, you can check a box to show these platforms. Additionally, we hide several columns for simplicity; however, similarly these can be displayed using the Column visibility option. This table can also be exported as csv or pdf.

Output

The Output tab provides the results for your sample and settings Input. Navigate here after you have modified the Input tab. Specifically, three tables are provided:

  1. Total Sequencing Needs:
    • This table provides a summary of the total sequencing needs per technology including number of samples, preps per sample, yield (Gbp) number of reads (millions), number of s-reads (millions), data storage needs (GB), and data storage cost (USD).

Column details

  • Details
    • Total samples
    • Total preps (per sample): Different technologies have different capabilities. For example, small variants and structural variants may require two separate library preps with short-read platforms compared to long-read platforms that can be done with one prep.
    • Yield (Gbp)
    • Number of reads (millions)
    • Number of s-reads (millions): S-reads is short for “segmented reads”. For certain applications, shorter reads can be concatenated together to increase throughput. The primary application is PacBio Kinnex for full-length RNA-Seq, scRNA, and 16S
    • File Size (GB): Different technologies store data in different ways. The way data is stored matters for planning computational infrastructure and storage costs.
      • Illumina SBS and PacBio SBB store data in fastq.gz format which averages 0.5 bytes/base. PacBio HiFi stores data in bam format which also averages 0.5 bytes/base. Oxford Nanopore stores data in fast5/pod5 format which averages 7.0 bytes/base.
    • Annual Storage Cost (USD): Storage cost given file size and AWS S3 storage cost of $0.023 per GB per month

  1. Experiment Breakdown
    • This table provides the same information as the Total Sequencing Needs table, but provides a breakdown of the data needed per sample and library prep/application.
    • This information is also provided as a plot to visualize the number of library preps needed and which data types can be run within the same library prep.
  2. Total Cost & Runtime
    • This table provides a summary per sequencing instrument of the number of runs, flowcells, lanes (if applicable), sequencing cost, and amount of time needed to complete the experiment in units of instrument runtime.
    • Rows are colored by sequencing technology and barplots are provided per column for easy comparison. Rows are sorted by sequencing cost from least to greatest. This table can also be exported as csv or pdf.

Total Sequencing Needs

Experiment Breakdown

Total Cost & Runtime