Supported file formats

Bioinformatics file formats

Below we list some of the common file formats supported by CLC Workbenches. For a detailed listing of the formats each particular CLC Workbench can import and export, please click on the links below:
CLC Genomics Workbench
CLC Main Workbench
CLC Sequence Viewer 
File type Suffix File format used for
ACE files .ace contigs
Phylip Alignment .phy alignments
GCG Alignment .msf alignments
Clustal Alignment .aln alignments
Newick .nwk trees
FASTA .fsa/.fasta sequences
GenBank .gbk/.gb/.gp sequences
GCG sequence .gcg sequences (import only)
PIR (NBRF) .pir sequences (import only)
Staden .sdn sequences (import only)
DNAstrider .str/.strider sequences
Swiss-Prot .swp protein sequences
Lasergene sequence .pro protein sequences (import only)
Lasergene sequence .seq nucleotide sequences (import only)
Embl .embl nucleotide sequences
Nexus .nxs/.nexus sequences, trees, alignments, and sequence lists
CLC .clc sequences, trees, alignments, reports, etc.
Text .txt all data in a textual format
CSV .csv tables, each cell separated with semicolons (only export)
ABI .abi trace files (import only)
AB1 .ab1 trace files (import only)
SCF2 .scf trace files (import only)
SCF3 .scf trace files (import only)
Phred .phd trace files (import only)
PDB .pdb structure (import only)
BLAST Database .phr/.nhr BLAST database (import)
VectorNTI Database   sequences (import of whole database)
VectorNTI archives .ma4/.pa4/.oa4 sequences (import only)
Gene Construction Kit .gcc sequences (import only)
RNA Structure .ct/.col/.rnaml/.xml RNA structures
Preferences .cpf CLC preferences
SOLiD .csfasta .qual See manual (import only)
Illumina .Fastq .Scarf .Qseq See manual (import only)
Roche 454 .fna .qual .sff Sequence data, Quality files. See manual (import only)
Ion Torrent .sff .fastq Quality scores are expected to be in the NCBI/Sanger format. See manual (import only)
BAM .bam See Sequence assembly files
CLC Assembly File .cas Output from the CLC Assembly Cell (import only)
SAM .sam See Sequence assembly files
Tabular assembly .aln/.txt/.bed See Tabular assembly files (import only)
Zip export .zip Selected files in CLC format
Selected files in CLC format .zip (import only)
Clone Manager .cm5 sequences
DS Gene .bsml (import only)
Raw sequence any Only sequence (no name)
Affymetrix CHP .chp/.psi Expression values and annotations (import only)
Affymetrix pivot/metric .txt/.csv Gene-level expression values (import only)
Affymetrix NetAffx .csv Annotations (import only)
GEO soft sample/series .txt/.csv Expression values (import only)
Illumina .txt Expression values and annotations (import only)
Generic .txt/.csv Expression values (import only)
Generic .txt/.csv Annotations (import only)
Please, note that CLC Genomics Workbench can import ‘external’ files, too. This means that all kinds of files can be imported and displayed in the Navigation Area, but the above mentioned formats are the only ones whose contents can be shown in CLC Genomics Workbench.

Graphics file formats

All CLC workbenches support export of graphics into a number of formats. This way, the visible output of your work can easily be saved and used in presentations reports etc.
Bitmap image files:
  • Portable Network Graphics (.png)
  • JPEG (.jpg)
  • Tagged Image File (.tif)

Vector graphics files:

  • Portable Document Format (.pdf)
  • Scalable Vector Graphics (.svg)
  • PostScript (.ps)
  • Encapsulated PostScript (.eps)

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