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Welcome to the Clinical Sequence Analyzer (CSA) user manual.

CSA is a web-based clinical decision support tool that allows users to quickly identify clinically relevant phenotype-associated genes and variants from individual patients or families.

In CSA, users can follow customized case workflows to set up a study, identify genes and variants of interest, perform variant curation and scoring according to ACMG guidelines, and generate clinical reports from study findings. CSA also provides direct access to Sequence Miner to immediately visualize raw sequence reads and highlight gene candidates.

This manual covers the basics of getting started with CSA; creating and managing studies, variant curations, and reports; and a Supplemental Resources section for further information about resources and references in CSA.

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