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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Notes There are no recorded dates and only record type Changed prior to v1.4.0. Also, no version tags existis prior to version 1.0.0. Pipeline scripts were only added to this repository starting from version 1.4.0.

1.5.0 - 2021-10-02

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

1.4.0 - 2021-01-27

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

1.3.3 - 2016-04-18

Changed

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

[1.3.2] - 2016-04-07

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)

1.3.0 - 2015-04-16

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

1.2.2 - 0000-00-00

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)

1.2.1 - 0000-00-00

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

1.2.0 - 2014-07-07

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

1.1.1 - 0000-00-00

Changed

  • extended: fix typo bug in create-index-last.sh
  • extended: quickstart manual update

1.1.0 - 0000-00-00

Changed

  • core: code cleanup
  • core: SEQAN update with faster alignments (>2x speed improvement)
  • core: indexed FASTA access (now runs on computers with much less RAM)
  • core: code speedup by factor of two
  • core: clean up command line options
  • core: improve packaging scripts
  • extended: workflow on workstations with limited memory (new indexed FASTA feature in taxator; with BLAST)
  • extended: switch to NCBI BLAST+ (nucleotide megablast) as default, option to use LAST
  • extended: general cleanup/improvement of included workflow scripts; no Python required any more in BLAST workflow

1.0.0 - 2013-08-19

Changed

  • core: publication release, many functionality 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

[0.3] - 0000-00-00

Changed

  • core: bug fix for noise filtering in binner
  • core: tools reduced to a core set around taxator (previously predictor) and binner (prevously predictions-filter)
  • core: multi-threading support in taxator
  • core: binner supports user defined identity constrains at fixed ranks

[0.2] - 0000-00-00

Changed

  • core: predictions-filter for combination of predictions by mutiple methods/experts and to clean up the predictions of natural samples where we require a certain number of read for each taxonomic group to be considered

[0.1] - 0000-00-00

Changed

  • core: functional framework with support for various LCA methods and fast aligners