Git repository for scripts associated with benchmarking study (https://doi.org/10.1186/s13059-017-1299-7)

Clarifications and notes brought to our attention:

• the kraken db build command in the manuscript is for the bacterial database; the command for the standard db is available through the kraken manual: kraken-build --standard --db $DBNAME (our database was constructed in July 2015)
• it should read Segata, et al. (2012) not (2013) in Table S2
• the abundances in the _abund.txt files within truth_set_relative_abundances.zip were provided by Nicola Segata for the LC and HC datasets here https://groups.google.com/forum/#!topic/metaphlan-users/UECjtMsMZEY
• Table S3 includes an abundance filter of 0.01