Version 3.1.0 [2024/08/26]

This includes the changes used in https://doi.org/10.1093/bioinformatics/btae097

Features

• Two new profiles: pairs-default and pairs-sensitive that are useful in combination with higher --num-matches. 6cd1d33
• Improvements to the core algorithm. 40b49a0

Notable bug fixes

• In edge cases, the alignment coordinates may have been calculated wrongly. f1ebc9a
• Proper exception handling. aad68eb
• Accept .fna and .faa as extensions for FASTA files. 05262cd

Compatibility

• The command line interface is compatible to 3.0.0.
• The on-disk format is compatible to 3.0.0.
• The output generated for most input files has changed slightly since 3.0.0.

Dependencies

• same as for 3.0.0

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.

Version 2.0.1 [2023/07/18]

features

• use --bit-score in addition to or instead of --e-value

bug fixes

• fix 32bit builds
• bug in BLASTN e-value calculation (slightly changed values)
• various typos and documentation fixes
• fix dispatcher script on macOS

compatibility

• the command line interface is identical to lambda >= 1.9.4
• the on-disk index format is compatible to lambda >= 1.9.3
• requires seqan >= 2.3.1; binary packages based on seqan-2.4.0
• compatible with C++17 if used with seqan >= 2.4.0

Release 2.0.0 [2019/01/11]

First stable release in the 2.x branch. It is identical to 1.9.5.

Pre-Release 1.9.5 [2018/05/30]

bug fixes

• BLASTN was broken (#115)
• wrong escaping of " and ' in command line arguments (#116)
• mixed lower-case / upper-case letters led to error on indexing (#117)
• divide-by-zero with very small databases (#118)
• lca-computation error with some certain sequences that have no taxonomy information (#119)

compatibility

• the command line interface is identical to lambda >= 1.9.4
• the on-disk index format is compatible to lambda >= 1.9.3
• requires seqan >= 2.3.1; binary packages based on seqan-2.4.0
• compatible with C++17 if used with seqan >= 2.4.0

Release 1.0.3 [2018/02/17]

bug-fixes and minor changes

• fix build with seqan-2.4.0 (#114)

compatibility

• both the interface and the generated index files are fully compatible to the 0.9.* and 1.0.* series
• requires seqan-2.2.0 or later

packages are due at a later point in time, if you want the stable branch, just use the binaries from 1.0.2

Pre-Release 1.9.4 [2018/02/05]

features and usability improvements

• all new single-executable interface with sub-commands (like git); see the LAMBDA → lambda2-guide (#88, #94)
  • the executable is now called lambda2
  • the subcommands mkindexp, mkindexn, searchp and searchn are currently supported
  • the -p/--program parameter has disappeared, instead one chooses via the command between nucleotide and protein search (#96)
  • many options are now auto-detected from the files, including all index-options and the source alphabets (DNA vs AminoAcid) (#6, #60)
  • all short options are now single-letter, some short-options specifiers where removed (#108)
• man-pages are now automatically generated and included in the packages
• generic and optimised binaries are now shipped within the same package and automatically selected
• index generation is now 30% – 50% faster (#112)

bug fixes

• crash on empty query sequences, fix requires seqan >= 2.4.0 (#111)
• crash if output file is placed given in non-existent or non-writable directory (#113)

compatibility

• the command line interface has changed considerably, please see the LAMBDA → lambda2-guide
• the on-disk index format is compatible to 1.9.3
• requires seqan >= 2.3.1; binary packages based on seqan-2.4.0
• compatible with C++17 if used with seqan >= 2.4.0

Release 1.0.2 [2017/06/29]

features

• lambda now informs you if updates are available, see Privacy for more details (#97)

bug-fixes and minor changes

• various fixes from new SeqAn versions

compatibility

• both the interface and the generated index files are fully compatible to the 0.9.* and 1.0.* series
• requires seqan >= 2.2.0 (pre-built executables based on seqan-2.3.2)

Pre-Release 1.9.3 [2017/06/29]

• everything from 1.0.2, including checks for updates

features and usability improvements

• faster searches through
  • two-step extensions for short reads (#36)
  • use of SIMD for short reads (#89)
• smaller indexes again, approx. the size before 1.9.2 (#93)
• species annotation (#76):
  • support for extracting RefSeq and UniParc accession IDs
  • support for UniProt .dat mapping files in addition to NCBI's .accession2taxid
• the expected memory usage is pre-calculated and checked against available (#86)

bug-fixes and minor changes

• fixed subject position error in some matches in 1.9.0 - 1.9.2 (#87)
• stricter parameter checking that prevents wrong usage with obscure errors (#92)
• better exception handling (#100)
• some fixes to BLASTN and TBLASTX modes (#95, #102, #104)
• rare crash on FreeBSD
• stack overflow on long exact matches (especially BLASTP, BLASTN)

compatibility

• the on-disk index format has changed and is not compatible to any previous version
• requires seqan >= 2.3.1 (packages built from seqan-2.3.2)

Pre-release 1.9.2 [2017/01/10]

• everything from 1.0.1

features

• SIMD parallelization for short query sequences, e.g. Illumina; not yet default (#58)
• species annotation of subject sequences, see Taxonomic Workflows (#63)
• compile time option that enables larger protein databases sequences (#70)
• bi-directional indexes supported; not yet default (#74)
• taxonomic binning, see Taxonomic Workflows (#77)

bug-fixes and minor changes

• crash when encountering input sequences that are shorter than a seed (#66)

compatibility

• the on-disk index format has changed and is not compatible to any previous version
• some of the optional --sam-bam-tags were renamed, see the wiki (#79)
• requires seqan-2.3.1