This guide covers the most important differences between lambda2 (1.9 - 2.0.1) and lambda3 (3.0.0+).

The command line interface is mostly unchanged from the lambda2 branch. However, some advanced options have been removed, and several new options have been added.

• Added the bisulfite sub-programs (lambda3 mkindexbs and lambda3 searchbs).
• A --bit-score VALUE option was added which can be used additionally to the e-value option. To use only the bit-score threshold and ignore the e-value, also set --e-value -1.
• Different presets/profiles are available with --profile fast and --profile sensitive.

See the --advanced-help page for details.

• Indexes are now stored as single files with the .lba extension.
• Compressed indexes are supported (.lba.gz). They are decompressed implicitly.