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Sequencing FilesOverview

Sequencing Files

SeqDesk monitors a configurable data directory for sequencing files. It automatically detects FASTQ files, pairs forward and reverse reads, and lets you assign them to samples — either automatically or manually.

File discovery and assignment are facility-admin only and live under an order’s Sequencing tab (/orders/[id]/sequencing). There is no standalone “Files” page: the legacy /orders/[id]/files route just redirects (facility admins to the Sequencing tab, everyone else to the order page). An order must be SUBMITTED or COMPLETED before sequencing data can be managed.

File Discovery & Auto-DetectDirectory scanning, R1/R2 pairing, naming conventions, and scan caching.Assigning Files to SamplesAuto-detect matching, manual assignment, and confidence thresholds.

The data directory path and scan settings are configured in Administration → Data Storage.