Benchling supports a wide range of file formats, including both common and proprietary ones. We’re constantly updating the formats we support, so just try dragging in your files into the importer – our goal is to have the importer “just work” regardless of the file format. If you ever run into any problems, please don’t hesitate to ask for help at firstname.lastname@example.org.
The most common two file formats are GenBank and FASTA. Benchling fully supports these two formats, so when encountering importer errors or trying to import sequences from an unsupported format, a quick workaround is to “save as” to either format as most applications can export either Genbank or FASTA.
The following formats are fully supported in Benchling – the sequence, annotations, and comments will all be directly imported into Benchling. To avoid import errors, please ensure your file names are written as shown in the table below. For example, if you are importing a file named "FILE" with multiple sequences using FASTA, the file name should be “FILE.fasta” so Benchling can recognize the file and upload multiple sequences separately.
Unsupported File Types
At the moment, Benchling unfortunately cannot parse out sequences saved as PDF or as Microsoft Word files (doc, docx). The easiest way to get these sequences into Benchling is to create a new sequence and then copy and paste in the bases.
- The file extension of the format. Benchling sometimes tries to guess the file format by extension, so if you ever encounter importer errors and the file extension doesn’t match the table, try renaming the file and then reimporting.
- Files in this column are archives that can potentially contain more than one sequence. When a multi-sequence file is imported, Benchling will automatically split the archive and import each individual sequence into your library. (Most other applications will ignore all sequences past the first, so the behavior may differ slightly).
- Files in this column are results from Sanger sequencing, and will contain chromatogram traces along with quality data when imported as an alignment.