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CHANGELOG.md

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Changelog

[2.1.2] - 2021-05-10

Changed

  • New retry behavior for kraken2-build --download-library --use-ftp

Fixed

  • Bug that caused classification to not work when k-mer length was equal to minimizer length
  • Missing source file in CMakeLists.txt

[2.1.1] - 2020-11-08

Fixed

  • Compilation error with GCC 10, omission of cstdint header
  • Removed --skip-maps from standard install due to addition of plasmids, which require acc/taxid maps

[2.1.0] - 2020-10-13

Added

  • Small viral reference set and read simulator for future testing
  • Build options to aid testing
  • Integration of HLL to estimate distinct minimizer counts

Changed

  • Build code now creates databases with deterministic MD5 sums by default; --fast-build option to kraken2-build introduced to access old behavior
  • Added plasmid library to standard installation set
  • Updated SILVA to release 138.1

Fixed

  • Modified build code to prevent insertion of minimizers with ambiguous bases
  • Bug where hit list output in quick mode used internal taxid (not external)
  • No more attempts to download "na" paths from FTP site
  • Runaway memory usage bug with unpaired classification (thanks to D. Cameron)
  • Modified estimation code to better handle small reference libraries

[2.0.9] - 2020-04-07 (beta)

Added

  • Expose --load-factor setting to kraken2-build
  • New --minimum-hit-groups option to kraken2

Changed

  • Require 2 hit groups (set of overlapping k-mers w/ same minimizer) to make classification by default
  • Allow build options to pass through to subsequent invocations (e.g., k-mer length for 16S DBs)
  • Removed env options for library downloads (no longer available from same NCBI location)
  • Updated SILVA to release 138

Fixed

  • Removed mention of --fastq-input from Manual
  • Made PE read identifier suffix trimming more restrictive (only on /1 and /2)
  • Bug where some reads would be classified with taxid 0
  • Bug that didn't allow kraken2-inspect to work with large databases

[2.0.8] - 2019-04-25 (beta)

Added

  • FTP downloading option for taxonomy/libraries (--use-ftp for kraken2-build)
  • Option to skip downloading taxonomy maps

Changed

  • Added lookup table to speed up parsing in MinimizerScanner class
  • Default parameters for minimizer lengths and spaces changed (spaces=7 for nucleotide search, length=12 for translated search)

Fixed

  • Linked space expansion value for proteins to constant used by MinimizerScanner
  • Reporting of taxids in classified-out sequence files
  • Confidence scoring bug associated with failure to leave some sequences unclassified
  • Reverse complement shifting bug, code made backwards-compatible with existing databases (newly created DBs will have fix)
  • NCBI taxonomy download error due to removal of EST/GSS files

[2.0.7] - 2018-08-11 (beta)

Added

  • Disk usage info to kraken2-build --clean
  • Memory allocation error message for hash table
  • Option for --max-db-size and hash downsampling
  • Multithreading to kraken2-inspect

Changed

  • Move to /usr/bin/env for perl scripts
  • Add DB loading message to keep people from killing processes early
  • Add flag files for resuming download of nucleotide accession map data
  • Converted lookup_accession_numbers script into C++ program w/ memory mapping
  • Clarified in manual that one or more libraries allowed for custom DBs
  • Silenced progress messages in C++ programs for non-TTY stderr
  • Taxonomy downloads switched to rsync from wget (ftp)
  • Removed '%' from reports

Fixed

  • Allow d/l of protozoa library w/ kraken2-build script
  • Filenames for SILVA database taxonomy info
  • Typo in manual for output format example
  • Corrected default space count in manual
  • Removed obvious race condition in --add-to-library functionality
  • Corrected behavior of --classified-out and --unclassified-out (no longer forcing .fq/.fa file extensions, respecting '#' in paired mode)
  • Usage message in kraken2-inspect
  • Taxonomy creation for 16S databases

[2.0.6] - 2018-06-13 (beta)

Changed

  • New DB summary info printed out w/ inspect script + --skip-counts option

Fixed

  • Now stripping carriage returns and other trailing whitespace from sequence data
  • Treating l-mers immediately following ambiguous characters as ambiguous until a full k-mer is processed
  • Bug in expansion of spaced seed masks that left spaces at end

[2.0.5] - 2018-05-21 (beta)

Added

  • New kraken2-inspect script to report minimizer counts per taxon

Changed

  • Kraken 2X build now adds terminators to all reference sequences

[2.0.4] - 2018-05-06 (beta)

Fixed

  • Improved portability to older g++ by removing initialization of variable-length string.

[2.0.3] - 2018-02-12 (alpha)

Added

  • Reporting options to kraken2 script (like Kraken 1's kraken-report and kraken-mpa-report)

Changed

  • Made loading to RAM default option, added --memory-mapping option to kraken2

[2.0.2] - 2018-02-04 (alpha)

Added

  • Low base quality masking option

Changed

  • Moved low-complexity masking to library download/addition, out of build process
  • Made no masking default for human genome in standard installation

[2.0.1] - 2018-01-01 (alpha)

Added

  • Low-complexity sequence masking as a default
  • UniVec/UniVec_Core databases to supported downloads
  • UniVec_Core & human in standard Kraken 2 DB
  • 16S DB support (Greengenes, Silva, RDP)
  • --use-names flag for kraken2 script
  • Priority queue to ensure classifier output order matches input order when multi-threading
  • Changelog

Changed

  • Reduced amino acid alphabet (requires rebuild of old protein DBs)
  • Operating manual

Fixed

  • kraken2 now allows compression & paired processing at same time

[2.0.0] - 2017-12-04 (alpha, initial release)