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Export data to a file

The following table shows how to export one or more consensus sequences or to export tabular data from a view in SeqMan Ultra.

Item to Export How To
Any version of the Project Report, Contig Report or Variants views With the view open, click on the Export data tool ( ) at the right of the header.
Features view With the Features view open, click on the Export data tool ( ) at the right of the header or choose the File > Export Data > Features > (Contig Name) command. The tabular data can be saved in either comma- or tab-separated value (.csv or .tab) formats.
Data or sequences from the Text, Table or Pairwise views Click on the Export data tool ( ) at the right of the Table view header. Select from the following:

  • Matches without Gaps – To export an ungapped FASTA (.fasta) file consisting of matching regions of displayed matches, but not the query sequence itself.

  • Aligned Matches – To export a gapped FASTA (.fasta) file with displayed matches aligned against the query.

  • Table – To save Table view contents in either Comma- or tab-separated value (.csv or .tab) formats.

  • Text – To save the Text view contents in Text (.txt) format.
Consensus sequences Select one or more contigs in the Explorer panel, then choose File > Export Data > Consensus > (Contig Name), File > Export Data > Consensus > Selected Contigs or Contig > Export Consensus of (Contig Name). Alternatively, from the Alignment view, use the Export data tool ().

In each case, the following dialog opens:




  • In the upper drop-down menu, choose Single File to save the reads in a single file with the name of your choice. Or choose Multiple Files to save reads in separate files.

  • Use the lower drop-down menu to choose the save format.

  • If you want SeqMan Ultra to remove consensus gaps when the contig(s) are saved, keep Include gaps unchecked (recommended). Check the box only if you want the gaps in the contig(s) to be retained.

  • Check Include Reference Only Bases as ‘N’ to export all bases that were only found in the reference sequence (not any of the constituent sequences) as Ns. An example in .fasta format is shown below.



  • Check Include Scaffold Position Information to include the position number in the header of the exported data file. If you check this box, the file header will including the text: /dnas_scaffold_POS=x where ‘x’ is the position of the contig in the scaffold.

    When you have finished choosing the desired settings, click OK.
Reads from a contig Select one or more contigs in the Explorer panel and choose Contig > Export Sequences of (Contig Name).




  • In the upper drop-down menu, choose Single File to save all selected read sequences in a single file with the name of your choice. Each contig in the file will begin with a note listing the contig name, scaffold ID and scaffold position. Or choose Multiple Files to save each selected contig as a separate file that is automatically assigned the same name as the contig.

  • Use the lower drop-down menu to choose the save format.

  • If you want SeqMan Ultra to include gaps when the contigs are saved, check the box next to Include Gaps.

  • To include masked based in the exported file, check the box next to Export entire sequence (includes masked bases).

  • To keep the orientation that was used when the read was aligned, check the box next to Preserve aligned orientation.

    When you have finished choosing the desired settings, click OK.

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