Glossary

Terms you might encounter

SMILE -> information associated with a sample. This is a current work-in-progress written in Java/Neo4J that is supposed to be the one source of truth for metadata associated with samples. Currently, these responsibilities are managed by Beagle.

LIMS -> Laboratory information management system -- when sequencing is complete, metadata and file information on the sequences is first input into this system.

Beagle -> triggers and monitors workflows. There's also a part of it that tracks files and metadata associated with those files which may be splintered out in the future. A request typically comes from LIMS which begins the workflow process.

Hermes -> a nicer interface for Beagle (sample workflow tracking) and soon the MDB (make updates to metadata)

Ridgeback -> An HTTP API for Toil which Beagle is reliant on for interacting with workflows.

Toil -> A workflow engine that interfaces well with LSF.

Voyager -> The suite of applications built by the Voyager team, including Ridgeback, Beagle, and Hermes.

HPC-> Distributed high-performance computing that's managed in-house. Most data processing and files are housed here.

LSF -> IBM's Platform Computing (Load Sharing Facility) tool for scheduling workflows on HPC. It has a suite of commands specific to managing workloads.

Common workflow language -> a YAML-like language for defining workflows.

Nextflow -> Reactive workflow framework and a programming DSL that eases the writing of data-intensive computational pipelines.

DNA-SEQ -> Sequencing of the Deoxyribonucleic acid (DNA)

RNA-SEQ -> Sequencing of the Ribonucleic acid (RNA)

MSK-ACCESS -> Cell-Free DNA assay for patients with solid tumors

CMO-CH -> Assay for profiling clonal hematopoiesis mutations from blood

MSK-IMPACT -> Assay for profiling patients tissue DNA for solid tumors

MSK-IMPACT Heme -> Assay for profiling patients blood DNA for Heme malignancies

Facets -> Allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing

WES -> Whole Exome Sequencing

WGS -> Whole Genome Sequencing

WTS -> Whole Transcriptome Sequencing

Illumina -> one of the companies that provides sequencing machine

Novaseq -> Type of sequencer from Illumina

Nextseq -> Type of sequencer from Illumina

Miseq -> Type of sequencer from Illumina

Hiseq -> Type of sequencer from Illumina

PacBio -> a company that sells instruments for long-read sequencing based on zero-mode waveguide

Oxford Nanopore -> a company that sells instruments for long-read sequencing based on Nanopore technology