The Tools menu function Export Sample Contig/SPEC Files can be used to export the assembly contigs of multiple samples to files (FASTA). It can also be used to to export parts of the metadata of sample into special files (SPEC) that can be automatically imported by SeqSphere+ when the contig files are later imported again.

The export can be started

  • for all samples of a project,
  • for a selection of samples defined by a sample search criteria, or
  • for the currently loaded samples
Export Sample Contig and SPEC Files dialog

The following options can be selected when exporting the files:

General Options

  • Export for selected samples contig files and SPEC files / only contig files / SPEC files
Defines which kinds of files should be exported.
  • Export only samples with sequence data / without sequence data
If enabled, it defines that files will only be exported for samples that have / have not assembly contigs.
  • Create sub-folder for each Project
If enabled, each file is written into an automatically created sub-folder with the name of the project to which the specific sample belongs.
  • Use Alias ID instead of Sample ID as name
If enabled, the field 'Alias ID' is used as file name. The 'Sample ID' will not be written to the file.
  • Replace whitespace characters by underscore in file names
If enabled, blanks in file names are replaced against underscore characters.

Contig Files Options

  • Include name in contig sequence names
If enabled, the sample names ('Sample ID' or 'Alias ID') are used for each sequence name in the exported contig files.
  • Export ACE/BAM files instead of FASTA if available
If enabled, instead of a FASTA file the ACE/BAM file of a sample is exported if it is available.

SPEC Files Options

  • Export procedure details/statistics into SPEC files
If enabled, for each exported sample the available procedure details and procedure statistics are written into the SPEC file.
  • Export epi metadata into SPEC files
If enabled, for each exported sample the epi metadata will be written into the SPEC file. By default the option without filtering is chosen to export all available epi metadata. The option with privacy filter can be used to export only a selection of the epi metadata.
  • Export tags into SPEC files
If enabled, for each exported sample the tags assigned to the sample are written in the SPEC file.