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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:

File typeSuffixFile format used for
ACE files.acecontigs
Phylip Alignment.phyalignments
GCG Alignment.msfalignments
Clustal Alignment.alnalignments
Newick.nwktrees
FASTA.fsa/.fastasequences
GenBank.gbk/.gb/.gpsequences
GCG sequence.gcgsequences (import only)
PIR (NBRF).pirsequences (import only)
Staden.sdnsequences (import only)
DNAstrider.str/.stridersequences
Swiss-Prot.swpprotein sequences
Lasergene sequence.proprotein sequences (import only)
Lasergene sequence.seqnucleotide sequences (import only)
Embl.emblnucleotide sequences
Nexus.nxs/.nexussequences, trees, alignments, and sequence lists
CLC.clcsequences, trees, alignments, reports, etc.
Text.txtall data in a textual format
CSV.csvtables, each cell separated with semicolons (only export)
ABI.abitrace files (import only)
AB1.ab1trace files (import only)
SCF2.scftrace files (import only)
SCF3.scftrace files (import only)
Phred.phdtrace files (import only)
mmCIF.cifstructure (import only)
PDB.pdbstructure (import only)
BLAST Database.phr/.nhrBLAST database (import)
VectorNTI Databasesequences (import of whole database)
VectorNTI archives.ma4/.pa4/.oa4sequences (import only)
Gene Construction Kit.gccsequences (import only)
RNA Structure.ct/.col/.rnaml/.xmlRNA structures
Preferences.cpfCLC preferences
SOLiD.csfasta .qualSee manual (import only)
Illumina.Fastq .Scarf .QseqSee manual (import only)
Roche 454.fna .qual .sffSequence data, Quality files. See manual (import only)
Ion Torrent.sff .fastqQuality scores are expected to be in the NCBI/Sanger format. See manual (import only)
BAM.bamSee Sequence assembly files
CLC Assembly File.casOutput from the CLC Assembly Cell (import only)
SAM.samSee Sequence assembly files
Tabular assembly.aln/.txt/.bedSee Tabular assembly files (import only)
Zip export.zipSelected files in CLC format
Selected files in CLC format.zip(import only)
Clone Manager.cm5sequences
DS Gene.bsml(import only)
Raw sequenceanyOnly sequence (no name)
Affymetrix CHP.chp/.psiExpression values and annotations (import only)
Affymetrix pivot/metric.txt/.csvGene-level expression values (import only)
Affymetrix NetAffx.csvAnnotations (import only)
GEO soft sample/series.txt/.csvExpression values (import only)
Illumina.txtExpression values and annotations (import only)
Generic.txt/.csvExpression values (import only)
Generic.txt/.csvAnnotations (import only)

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)