Calculating Basespace Run Summary Metrics From Interop Sav Binary Files

Question

[ryan.ong8]

Hello,

In attempt to create a tool that will regularly report sequencing machine status and statistics, access to the following data is required for every lane and read:

R1 Phasing, R1 Prephasing, R2 Phasing, R2 Prephasing, R1 PhiX Error %, R2 PhiX Error %, # Raw Clusters, PF %

This data was available in the form of read XMLs generated by machines prior to the HiSeq 2500. However, with the HiSeq 2500 these XMLs have been replaced with SAV binary data files. The BaseSpace Run Summary page outputs the very information that I require, however it runs on Windows and my tool is not compatible.

I am able to parse the SAV binary files to get SAV metrics and metric codes. I would like to know how I can use these metrics to calculate the values that are output by the BaseSpace Run Summary.

Below is an example of Illumina's old HTML run report, which contains the information that I need and hope to calculate.

Thank you in advance.

Answer 1

[Mr. Dave]

For those searching, Illumina released InterOp libraries in 2016 to parse the SAV binaries.

Illumina InterOp Documentation

The libraries include a few programs in addition to C++ libraries. I believe index-summary can provide the data the original poster was seeking.

Other parsers that predate InterOp:

• Bio::IlluminaSAV (PERL)
• savR (R, Bioconductor)
• illuminate (Python)