The following table compares the functionality offered by Goby, BAM, CRAM and FASTQ formats. Please let us know if you think the table should be expanded to include other specific features.
(1) This line compares the ability of each file format to store full read bases. BAM and FASTQ provide this functionality as well as the Goby compact-read format. Neither the Goby alignment format nor CRAM support storing all read bases. The checkbox for Goby 1 and 2 indicates that Goby provides one file format that can store this type of information.