v1.5.0: major release

Taxator-tk can now classify protein input, a sample pipeline is included in the extended version. The overall memory consumption has been reduced.

Added

• core: taxator RPA algorithm with protein sequences
• core: taxator reduce memory usage with large fasta index and taxonomy mapping
• core: binner supports query globbing via regular expression to implement whole-genome binning
• core: add transparent gzip compression of taxonomy dump files
• extended: new sample pipeline using protein alignment with orfM and blastp

v1.4.1: bugfix release

Fixed

• core: compile with recent compiler and Boost CMake detection

v1.4.0: major release

The repo now tracks both the core and extended versions, making it easier to reproduce. The documentation was aligned with common standards and many dependencies were updated to more recent versions. The release also contains minor bugfixes and speed improvements.

Added

• all: reorganized code and included extended pipeline scripts and documentation

Changed

• core: backport of code changes from 1.5 branch
• core: add version flags to binaries
• core: seqan update to v2.4.0
• core: tree.hh update to v3.7
• extended: correctly detect Python2 version with two digits in patch number
• extended: update KronaTools to v2.7.1
• extended: update GNU parallel to v20201222
• extended: align with LZA v1.9.3
• extended: align with NCBI Blast 2.11.0+
• extended: align with last-align v1170
• extended: parallel index building and ambiguous characters with last aligner

v1.3.3: bugfix release

Fixes bugs introduced in 1.3.2

Changed

• core: fix crashes in all LCA algorithms
• core: more consistent behavior of command line parameters in taxknife
• core: better error reporting

v1.3.2: bugfix release

Mainly improvements for the extended version scripts. Core fixes problems with the LCA algorithms and improves general error handling.

Changed

• extended: set more options via variable with LAST and BLAST
• extended: refactor shell code for cleaner workflows and improve POSIX compatibility
• extended: better CPU core detection via numproc command (supports containers)
• extended: specification of output folder (backward-compatible behavior)

v1.3.0: major release

Large effort have been taken to improve the software when applied to large real-world datasets. We use the well-specified Bioboxes binning format as standard output.

Changed

• core: rewrite of RPA with better handling of input alignments and speed improvements
• core: C++11 compatibility
• core: exception handling
• core: bioboxes output format
• core: suppress some notifications
• core: much better scaling core algorithm due to homolog selection heuristic, there is no need to restrict the number of input alignments any more
• extended: CPU core auto-detection, now working with Linux taskset/cpusets
• extended: support for multi-core alignment with LAST (lastal-parallel wrapper script)
• extended: support of parallel search with LAST by integration of GNU parallel in script lastal-parallel, uses lz4 compression of temporary data
• extended: faster conversion by integration of GNU parallel in script lastmaf2alignments-parallel
• extended: integration of KronaTools for interactive pie chart plotting
• extended: download script for sample refpack removed, the project page will point to a location from where to download refpacks

v1.2.0 to v1.2.2: major release and extended version improvements

We did extensive runtime optimizations, reorganized command line tools and improved build scripts. The extended version pipelines were improved considerably.

v1.2.0

Changed

• core: program taxknife substitutes name-filter and rank-filter
• core: adjust data types to support longer segments
• core: better approximation of identity scores + support values in binner
• core: optimizations in RPA procedure
• core: heuristic to avoid excessive runtime with bad alignments
• core: workaround for CMake bug with boost threads linking

v1.2.1

Changed

• extended: fix bug in binning-workflow-fasta-last.sh, reference FASTA index wasn't used
• extended: replaced quickstart.pdf by a text-based README file

v1.2.2

Changed

• extended: make reference data and aligner index location independent of installation root (easier to run it in multiuser environments)
• extended: remove integrity check for data (should become part of the refpack)
• extended: rename and clean all scripts
• extended: change standard BLAST algorithm to "discontiguous megablast" for better sensitivity (increases the runtime by ~20x)

v1.0.0: major release

The program version that was used in the publication.

Changed

• core: publication release, many functionalities added; evaluations done on this version
• core: optimized for large-memory systems
• extended: sample workflow shell scripts for taxonomic binning includes microbial RefSeq with taxonomy
• extended: large prepared LAST index with download script