GSI Best Practices

GSI has several best practices pipelines depending on the type of data sequenced. Our standard pipelines are for human tumour-normal matched samples, but these may vary by project requirements

Alignment and Polishing

Alignment is performed on a per-lane or demultiplexed library basis. We then merge multiple libraries if applicable and clean the data for subsequent analysis.

Type of Sequencing

Alignment (by library)

Data Polishing (by library or merged)

Illumina DNA (whole genome)

BWA mem

Filter mouse: Xenome or Xenoclassify

Merge lanes and mark duplicates: Picard

Realign indels and recalibrate base quality scores: GATK

Illumina DNA (all types)

BWA mem

Filter mouse: Xenome

Filter adapters: CutAdapt

Mark duplicated: Picard

Realign indels and recalibrate base quality scores: GATK

Illumina RNA (all types)


Nanopore (all types)

Alternate software can be substituted upon request.

Variant Calling, Transcriptome Analysis

Variant calling and transcriptome analysis may be included in the base analysis cost but still must be discussed with GSI's Bioinformatics Support Team. Other software may be available upon request.

Further Analysis

Do you have specific analysis needs not covered above? Reach out to us and we'll be happy to discuss them with you. Our team can help you take your samples from sequencing through to publication.

Contact The Genome Sequence Informatics Team

Morgan Taschuk

Director, Genome Sequence Informatics

Genome Sequence Informatics

morgan.taschuk at

Ontario Institute for Cancer Research (OICR)

MaRS Centre
661 University Avenue
Toronto, Ontario M5G 0A3