Optimizations

Can I speed up JBrowse load time with VCF and BAM files

If the BAM and VCF files you have are large, the BAM index or TABIX index files can become large as well. Since the indexes must be fully downloaded before any of the data can be displayed, you can break your files up by chromosomes, and use {refseq} in a urlTemplate to break it up into manageable chunks.

E.g.

"urlTemplate": "myfile_{refseq}.bam"

That would search for myfile_chr1.bam and myfile_chr1.bam.bai when you open that track while browsing chr1

Can I speed up generate-names.pl?

Try using --completionLimit 0 with the command. It will disable autocompletion but still allow you to search exact matches.

Note that you can use generate-names with --completionLimit 20 on some tracks and then generate-names with both --incremental and --completionLimit 0 flags on very information dense tracks.