Code commit

.gitignore

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+*.o
+src/build_db
+src/classify
+src/estimate_capacity
+src/dump_table

CHANGELOG.md

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+# Changelog
+
+## [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)

LICENSE

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-MIT License
+The MIT License (MIT)
 
-Copyright (c) 2018 Derrick Wood
+Copyright (c) 2017-2018 Derrick Wood
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

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+kraken2
+=======
+
+The second version of the Kraken taxonomic sequence classification system
+
+Please refer to the Operating Manual (in docs/MANUAL.html) for details on
+how to use Kraken 2.