Bioinformatics services for research use only (RUO) are offered in three levels of data analysis and return, with increasing costs. We also have accredited assays for clinical trials.

Types of RUO analysis:

  • Raw data (Fastq) : we return only the sequence data in Fastq format. Choose if you have a non-standard or non-human reference (e.g. T2T or mouse), or if you have your own bioinformatics team.
  • Aligned sequence : we return sequence aligned to the human reference (hg38) in BAM or CRAM format. Choose if you have specific bioinformatics analysis you want to run that’s distinct from our full packages.
  • Full package: we return all of our standard analysis types for your sequencing choice, which may include: fastqs, BAM/CRAM, somatic variant calls, copy number calls, etc. Note that some sequencing types have less in the full package than others, and you will be charged accordingly. Details for each sequencing type are below.

FULL PACKAGES

  • Shallow whole genome: BAM files, ichorCNA results
  • Whole Genome: Pre-processed call ready BAMs, Somatic variants, Structural variants, Copy number variants
  • Exome: Pre-processed call ready BAMs, Somatic variants, Copy number variants
  • Targeted sequencing/Panels: Aligned BAMs, UMI Deduplication, Somatic variants
  • smMIPs: Fastq files
  • cfMeDIP: Fastq files
  • Nanopore epigenome: BAM files
  • Transcriptome: STAR BAM files, RSEM expression, STAR-Fusion fusion calls
  • Nanopore transcriptome: Aligned BAMs

We return data to you in different ways depending on the service requested. Clinical reports are always returned through the Genomics Requisition System. We can provide genomic data via SFTP or rsync download or upload. We also provide data deposition services to EGA or cBioPortal

Finally, we can accept data sequenced elsewhere (“Bring your own data”) for analysis through one of our packaged services. Please contact us for a quote.

Illumina Fastq Generation

Generation of fastq files from Illumina run folders. This is run on all samples from illumina run folders generated through the genomics group, and data return is included as part of the sequencing costs

Alignment Only Pipelines

lane level alignments for DNASeeq against hg38 (merging of lanes is part of the preprocessing workflow) splice aware alignment and merging of whole transcriptome sequence to hg38

Alignment + Preprocessing : DNA Sequencing

call ready alignments

Whole Genome, Somatic Variant Calling Pipeline

Adapter Trimming Lane-level alignments Call-ready alignments (merged lanes) variant calling : snvs, short indels copy number calling structural variant calling

Whole Transcriptome RNASeq Analysis Pipeline

Splice aware alignment Transcript Quantification

WGTS Pipeline (Whole Genome, Transcriptome)

see above ; this is a combination of 1, Whole Genome Somatic Variant Calling Pipeline 2. Whole Transcriptome RNASeq Analysis Pipeine for samples from the same Donor/Case

Whole Transcriptome, Immune Analysis Pipeline

Whole Exome, Somatic Variant Calling Pipelline

Targeted Sequencing Panels Variant Calling Pipeline

Targeted Sequencing Libraries, with UMI incorporation

Shallow Whole Genome Analysis Pipeline

shallow whole genome copy number calling