Centrifuger v1.0.5

• Support output unclassified reads and classified reads through options "--un" and "--cl".
• Add the --size-table option to centrifuger-inspect.
• Improve the efficiency on more platforms.

Centrifuger v1.0.4

• Support creating the index for GTDB (https://github.com/mourisl/centrifuger/tree/master/indices#gtdb)
  • A pre-built index for GTDB r220 representative genomes is available at: https://www.dropbox.com/scl/fo/wtsermtdd62n1ttryuhwv/ADWTYiJA6Dh5gdbHmwC2nfo?rlkey=fgdpthjukcj1uhsjrcv35j927&dl=0
• Fix a serious bug in the silva-download.pl script
• Support the file to tax ID mapping through the "-l" option. This removes the need to create the sequence ID to tax ID mapping file
• Improve the index building efficiency
• When calculating the LCA, force the assignment to the root if it goes beyond the superkingdom level (#9 )
• Fix a serious bug in centrifuger-download when multi-threading (#8 )

Centrifuger v1.0.3

• Add the options to specify read sequences, barcode, and UMI, to work with barcode-based single-cell data.
• Update the "Makefile" in the indices folder to work with the contaminants sequence database.

Centrifuger v1.0.2

• Improve index building time-efficiency by implementing the Larrson-Sadakane algorithm for sorting suffix array elements of the difference cover
• Add the option to internal merge read pairs and remove adaptors, which could be useful for short fragment size data sets
• Improved running efficiency using a medium number of threads

Centrifuger v1.0.1

• Add the script to download and prepare Silva database
• Improve the speed when using many threads (>12)
• Fix several internal parameters to be more consistent with Centrifuge

Centrifuger v1.0.0

Initial release