lambda-v0.4.0

performance changes in comparison to published version (0.2)

• new default mode with 30-80% speed gains and up to 75% memory reduction over published version
• double-indexing mode with speed gains > 100%
• sensitivity slightly increased at the same time (1-2%)

changes in command line interface

• renamed many parameters and changed some defaults
• please look at lambda --help to see all the changes!!
• better control of verbosity with -v parameter
• threads now controlled with -t instead of environment variable

new features

• BlastN mode now usable again and proper parameter-handling added for it
• added percent identity cutoff in addition to e-value cutoff (-id)
• added a limit for maximum number of matches per query sequence (-nm)
• added abundancy heuristic (-pa) and priorization of hits to not look at all hits if number of hits >> chosen limit
• single-indexing mode which has huge memory advantages (-qi none) [now default]
• FM-Index is now also default
• removed Lambda-Alphabets, since they currently provide little benefit over Murphy10

bug-fixes and minor changes

• indeces with different settings (index type, alphabet) can now be created on the same fasta file without conflicts between them
• changed pre-scoring heuristic to include region around match (-ps and -pt)
• fixed build issues with gcc-4.8.x
• FastQ support fixed

availability

• Linux Binaries 64Bit
• Linux Binaries Sandybridge
• Source code (tarball)
• Source code (git)