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