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 format Goby 1.x Goby 2.0 BAM CRAM 0.7 FASTQ Supports non-sorted alignments N/A Supports storage of reads and their quality scores (1) Can store read meta-data N/A Maintains a link between alignments data and read data N/A Multi-tier data organization N/A Supports import-export of BAM data serious fidelity issues some 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/origin N/A Can store all BAM attributes/tags N/A Reference-based compression N/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 conversion N/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.