Intro to Ultima Bioinformatics
Get Started Analyzing your Ultima Genomics Data
Analysis Best Practices for our most popular applications including Whole Genome sequencing including: ppmSeq, germline WGS, somatic WGS, single-cell, proteomics, and RNA-seq
Regardless of application sequencing generates fluorescent signal. Primary analysis, which converts that flourescent signal into basecalls, is carried out automatically on the UG100 sequencing platform.
Secondary Analysis is application specific and processes the raw basecalls through several steps into the expected output file for interpretation or further downstream analysis depending on the workflow.
Secondary analysis tools on the UG 100 sequencing platform are application specific and optimized for Ultima's sequencing chemistry:
Trimmer divides each read into different segments and processes each segment, including pass-through, trimming, as well as barcode and adapter matching. Information about each segment can be written to configurable SAM tags.
Reads are tagged (barcodes, UMI, insert, etc.) and aligned (if the specified application requires alignment to a reference) –multiple references are available on the UG 100 platform.
Reads are sorted, demultiplexed, and de-duplicated.
For more information on Realignment with Ultima Aligner (UA):
Application-specific QC files are generated.
Data output is sorted, per sample, into folders based on the sample barcode used for demultiplexing.
Read data is output in a variant calling-ready CRAM file or an application-specific FASTQ file ready for third-party analysis tools.
For more information on Run Output Structure per application on the UG 100 sequencing platform see: UG Run Outpul Structure Reference
For more information on Supported Applications on the UG 100 sequencing platform see: UG Supported Applications Guide
Guides, Tutorials and GitHub Links
- WGS Germline
Ultima utilizes Efficient DV, an analysis pipeline designed to call variants from aligned CRAM files using a version of DeepVariant (DV) adapted for Ultima Genomics data. This section also covers germline CNV and structural variant (SV) calling pipelines.
Link to Germline WGS Dataset
- WGS Somatic
Ultima utilizes Efficient DV, an analysis pipeline designed to call variants from aligned CRAM files using a version of DeepVariantadapted for Ultima Genomics somatic data. This section also coversthe structural variant (SV) pipeline.
Access Somatic Variant Calling App Note
Link to Tumor/Normal Dataset
Learn More
- ppmSeq
ppmSeq or paired plus minus sequencing, is Ultima's ground-breaking WGS method to achieve accuracy of one part-per-million or better for calling SNVs via sequencing of both strands of a template molecule. ppmSeq identifies and removes disagreement between strands of a captured DNA molecule caused by sample errors. ppmSeq experiments on the UG 100 sequencing platform will output a variant calling-ready CRAM file as well as a ppmSeq-specific QC file.
Access ppmSeq Analysis App Note
Read the Tutorial on Conducting ppmSeq Analysis with our dataset
- RNA-Seq
RNA-Seq on the UG 100 sequencing platform outputs an unaligned CRAM file that is ready for input into downstream alignment tools such as Spliced Transcripts Alignment to a Reference (STAR) - https://doi.org/10.1093/bioinformatics/bts635
For detailed instructions on implementing STAR analysis please visit: https://github.com/alexdobin/STAR/blob/master/README.md
Access RNAseq App Note
Link to RNAseq Dataset
- Methylation
Whole genome methylation sequencing on the UG 100 sequencing platform includes read trimming, alignment (using a methylation-aware reference), and sorting.This is followed by automated on-instrument secondary methylation analysis using MethylDackel (https://github.com/dpryan79/MethylDackel/blob/master/README.md) which provides output of methylation statistics and QC information.
Access Methylation Variant Calling App Note
Link to Dataset
Learn More
- Single-Cell
Single cell and spatial analysis on the UG 100 sequencing platform include file output structures tailored for direct input into downstream analysis tools specific for supported assay preparation kits.
Link to 10x Genomics App Note
Link to Parse Biosciences App Note
10x Genomics Visium HD dataset
Link to Parse Biosciences dataset
Learn More
- Olink
Ultima Genomics’ UG 100 sequencing platform provides on-instrument analysis support for Olink proteomics libraries including sequence matching of Olink forward and reverse barcodes to reference whitelists. The identified forward/reverse barcodes are tabulated to generate a counts file (hist.csv) that is designed for input directly into Olink’s NPX analysis software - https://olink.com/software/npx-software.
<link> Link to Olink App Note