Overview

SPEC files can be used in SeqSphere to export and import Metadata together with sequence data files. There are different purposed where they are useful:

• Exporting/importing contig files from Samples together with metadata

The menu function File | Export Sample Contig/SPEC Files can be used to export the FASTA assembly contigs for multiple Samples. By default this also stores a separate SPEC file for each FASTA file, with the same name but extension ".spec". If exported FASTA files are later imported by SeqSphere+, the SPEC files are automatically detected and imported as procedure details and statistics. Optionally, metadata and tags can also be exported/imported using SPEC files.

• Exporting/importing predefined procedure details

Laboratory and assembly procedure details can be predefined and managed using the menu function Options | Procedure Details. The predefined sets can be exported to SPEC files. They can also be imported from SPEC files that were exported from existing Samples in the Procedure tab.

• Storing Metadata for Downloaded FASTQ Files

The menu function Tools | Download FASTQ from SRA can be used to download FASTQ files from NCBI SRA. The metadata of downladed runs, is automatically stored in SPEC files that are in the same directory as the FASTQ files.

• Forwarding procedure details and statistics from an external assembling pipeline

If an external assembling pipeline outside of SeqSphere+ (e.g., HGAP) is used to create contig files for later import into SeqSphere+, the SPEC files can be used to hand over assembly statistics. The SPEC files must be located in the same directory as the contig files, and they must have the same names as the contig files, but with the extension ".spec". They are then automatically processed by SeqSphere+ together with the contig files (fields see below).

A description of the SPEC-file format can be found on the page Import of Metadata.