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.
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
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