Bracken v2.9

This release addresses changes to kraken-uniq, no longer allowing input files to be streamed in for classification. The update now concatenates all library files and then classifies the library to generate database.kraken

Bracken v2.8

Bracken now works with KrakenUniq. Users can specify bracken-build -y krakenuniq to create krakenuniq kmer_distribution files. Krakenuniq reports will also work with Bracken.

Bracken v2.7

Clades without genome-level assignments will no longer be removed.

Bracken v2.6.2

Small updates thanks to @milot-mirdita

Bracken v2.6.1

Bracken is now compatible with KrakenUniq and Kraken2Uniq reports.

Bracken v2.6.0

kraken_processing.cpp has been modified to accommodate a smaller RAM machine and to be faster. The two previous steps for reading database.kraken and generating the new databaseXmers.kraken file have been combined into a single I/O step to avoid requiring the entire database.kraken file to be read into memory.

Bracken v2.5.3

Remove need for -w specification when running bracken
Update versioning

Bracken v2.5.2 - Fixes for bugs + Support for non-traditional taxonomy abundance estimation

Made some fixes to the code to accommodate non-ncbi taxonomy files. Also made changes to allow for non-traditional taxonomy abundance estimation (such as estimates at levels R5, R6, G1, G2, S1, S2, etc). Also some debugging to make sure the build files are consistent/accurate.

Bracken v2.5 - 30x Faster bracken-build time

Bracken-build script kraken_processing.cpp updated/optimized to allow for 30x faster build time (as tested on 1 Million DB sequences and 16 Threads)

Bracken v2.2

fixing version numbers