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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 a sequencing 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 sequencing order page). A sequencing 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.