Read mapping formats

File type Suffix Import Export Description
ACE .ace X X No chromatogram or quality score
AGP .agp/.fa   X Exports scaffolded contigs (see below)
BAM (Compressed version of SAM) .bam X X See SAM import
CLC .clc X X Rich format including all information
CLC Assembly File .cas X   Output from the CLC Assembly Cell
SAM (Sequence Alignment/Map) .sam X X See Sequence assembly files
Zip export .zip   X Selected files in CLC format
Zip import .zip X   Contained files/folder structure
Special note about AGP format: both sequence lists and contigs with reads mapped can be used. Based on annotations of type Scaffold (which are automatically added when running the de novo assembly with the scaffold option), the contigs are broken up before exported as fasta. The agp file produced holds information about how the contigs relate to each other.