Link or Upload Assembly Files

When importing WGS data into SeqSphere+, only the found targets and the contig files (FASTA) are always stored in the database. For the assembly files (ACE/BAM) there are two option to associate them to the Sample:

  • Store only a link to the original file
Only the path of the file, as it is seen from SeqSphere+ client computer, is stored together with the Sample. This has two consequences: Another SeqSphere+ client computer can only use those file links, if they refer to a network attached storage (NAS). And the assembly data is not available for re-analysis any more if the original file is deleted.
  • Upload the file to the server
The assembly file is stored on the SeqSphere+ server and is therefore accessible from all SeqSphere+ client computers. However, this requires a large amount of disk space on the server or connected NAS (~200 MB per Sample, see more details).

When creating Samples from assembled genomes or when defining a pipeline, it can be specified if the assembly data files should be linked or uploaded.

Managing Files of a Sample

The Procedure tab of the Sample Overview

The files that are associated to a Sample can be controlled, exported and removed in the Procedure tab of the Sample Overview.

There are different types of files:

  • Scanning Procedure Details
This is a detailed description of the parameters that were used in the allele calling process. It can be exported as a field of the Procedure Details.
  • Assembly (ACE/BAM/FASTA)
The assembled gnome file that was used as input when scanning and importing targets for this Sample. The Procedure Details for this file are shown in a table below (right-click to export).
  • Raw Reads (FASTQ)
If the data was assembled in a pipeline, than the links to the original raw read files are listed.
  • Contigs (FASTA)
If the Assembly file contains the assembled reads, than the plain assembly contigs are stored additionally in an extra file. This is useful when the assembly contigs should exported for further external usage.
  • Comments
If the Sample was created by a pipeline, the pipeline log messages for this Sample are listed.