add SINGULAR to platform tags

[omicsorama]

This request is to add Singular Genomics SINGULAR to list of platforms

[jkbonfield]

Thanks for making this PR. It seems like a trivial but totally worthwhile addition. We'll get it on the next GA4GH "File Formats" meeting (6th Dec) if not resolved before then.

+1 from me though.

[omicsorama]

thanks!

[jmarshall]

As in the similar recent #648 (comment) and #651, it would be good to provide (for posterity) a little background as commentary on this PR.

Apologies if this is obvious and I am simply unaware, but: is your sequencing technology generally available at present? Are there papers you can point us at that perform an analysis based on Singular data? Can you point us at sequencing data made available by such papers or projects, or say something about the expected timelines for general availability for running samples on your instruments? (The informal checkbox I'm trying to tick off here is “to be listed, platforms should be available and in use”. i.e., we try to avoid adding platforms that don't eventually make it to market or see significant third-party usage.)

[jkbonfield]

I can answer part of this. The machine data is available here, and the most recent publication is here. They claim to have started shipping in May 2022, and have a quoted lead time of 4-8 weeks for new installations. So it feels like a sensible candidate.

Obviously Element Biosciences can comment further on the availability.

(Edit: it would be nice if data was available as an aligned BAM instead of FASTQ, as it's a bit of added inertia to be bothered to download and align the whole thing just to look at a few regions and eyeball it. I did an alignment of a small portion - hence shallow - just to get stats on accuracy and it's looking like a contender.)

[blajoie]

Obviously Element Biosciences can comment further on the availability.
@jkbonfield - I think you meant Singular. Singular (G4) and Element Biosciences (AVITI) are separate technologies, instruments and companies :)

[jkbonfield]

Argh, you're quite right. I'm mixing my systems up terribly! My apologies to both Singular and Element Biosciences (who are already in there).

As for Singular - I don't yet know about data other than their tech report (NA12878 validation, but no link to downloads) or instrument availability.

[nh13]

@jkbonfield can you please re-review?

[jmarshall]

It would be great if some Singular folk could provide some pointers in reply to the questions in #686 (comment).

[shultzaberger]

Hi @jmarshall. Thanks for your help. The Singular Sequencer (G4) is available and we have begun shipping. There are applications notes for Bulk RNA-Seq, scRNA-Seq, Whole Human Genome + Exome sequencing with germline variant detection on the Singular website here: https://singulargenomics.com/resources/ . For now, accompanying data for all tech reports are available for download by request (email [email protected] and someone will send a download link), but we are working to moving those data to be directly downloaded through the website. Links to download some of those data sets directly are given below:

RNASeq: https://singular-public-repo.s3.us-west-1.amazonaws.com/RNASeq_repo/RNA_seq_fastq.tar
scRNA: https://singular-public-repo.s3.us-west-1.amazonaws.com/scRNA_v2_repo/Singular_scseq_TechReport_Fastqs.tar
human WES: https://singular-public-repo.s3.us-west-1.amazonaws.com/Singular_WES_TechReport_Repo/Singular_WES_TechReport.tar

Please let me know if you need any additional information or have any issues accessing data. Thanks again

[github-actions]

Changed PDFs as of 0dd3e0d: SAMv1 (diff).