Version 3.0.0 [2023/07/25]

This is the first release of the new lambda3 branch. It is much faster, offers new features but is not compatible to previous versions.

Version 3.0.0 [2023/07/25]

Features

• New program mode for searching bisulphite data.
• The nucleotide mode has received much more testing and optimisation.
• Huge overhaul of the algorithm; Lambda3 is up to 3x faster than Lambda2 and uses less memory.
• Use --profile fast or --profile sensitive to select finetuned parameter combinations that are faster or more sensitive than the default.

Compatibility

• The command line interface is very similar to Lambda2's, but some options have been added and some removed.
• The on-disk format of the index has changed. You need to recreate your index files or download new ones from the wiki. Indexes are now single files and may be used in compressed state.
• GCC-11 or later and -std=c++20 is required to build.
• Requires 64bit Intel or AMD CPU with SSE4 and POPCNT instructions.

Dependencies

• SeqAn 2.4.1; SeqAn3 is not used anymore
• BioC++ Core 0.7.1
• BioC++ IO
• Cereal 1.3.2
• ShargParser-1.0.0
• fmindex-collection
• all of these requirements are only required at build-time.