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.

Feature / File formatGoby 1.xGoby 2.0BAMCRAM 0.7FASTQ
Supports non-sorted alignmentsN/A
Supports storage of reads and their quality scores (1)
Can store read meta-dataN/A
Maintains a link between alignments data and read dataN/A
Multi-tier data organizationN/A
Supports import-export of BAM dataserious fidelity issuessome fidelity issues
Piled-up mode (stores quality scores at positions where at least x non-reference bases were observed).N/A
Can store soft-clipped bases and their quality scores
Can store all read quality scores
Can store read names
Can store read groups/originN/A
Can store all BAM attributes/tagsN/A
Reference-based compressionN/A
GZip compression (fast compression/decompression)
BZip2 compression
Nimble schema evolution (edit schema, recompile, ready to go)
Hybrid Structured Data Compression
Visualize with IGV without conversionN/A
Native analysis pipeline(s)

(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.