3.5 Exporting files

To export files from Geneious Prime, select the file or files you want to export and click File Export Selected Documents. Each data type has several export options, as detailed in the table below. Any set of documents may be exported in Geneious native format, and these files are back-compatible to Geneious version 6.0 (e.g. Files exported in .geneious format from Geneious R7 and above can be imported to Geneious R6 or later).

If you wish to export the parents and/or descendants of a particular file at the same time, choose File Export with Parents/Descendants.

Data type Export format options

DNA sequence FASTA, Genbank (XML or flat), CSV/TSV, Geneious
Amino acid sequence FASTA, Genbank (XML or flat), CSV/TSV, Geneious
Chromatogram sequence ABI, Geneious
Sequence with quality As above, also FastQ, Qual
Annotation GFF, BED, Genbank, Geneious
Alignment or Assembly Phylip, FASTA, NEXUS, MEGA, Phrap ACE, SAM/BAM, Geneious
Variant calls VCF (single sample only)
Phylogenetic tree Phylip, FASTA, NEXUS, Newick, MEGA, Geneious
PDF document PDF, Geneious
Publication EndNote 8.0, Geneious
Graphs CSV, WIG
Document Properties CSV, TSV, Geneious
Text files .txt, CSV, TSV, Geneious
Assembly report .html

Documents imported in any chromatogram or molecular structure format can be re-exported in that format as long as no changes have been made to the document.

Both fasta and fastq files can be exported in compressed (fasta.gz and fastq.gz) format for smaller file size. If exporting paired reads in fasta format, an option to export the forward and reverse reads to separate files is available by choosing ’Fasta Paired Files’ as the file type option.

   3.5.1 Export to comma-separated (CSV) or tab-separated (TSV) files
   3.5.2 Exporting multiple files
   3.5.3 Drag to desktop Genbank export