KrakenTools is a suite of scripts to be used alongside the Kraken, KrakenUniq, Kraken 2, or Bracken programs.

These scripts are designed to help Kraken users with downstream analysis of Kraken results.

Usage

kraken_tools(script, ..., python = NULL)

Arguments

script

Name of the kraken2 script. One of "combine_kreports", "combine_mpa", "extract_kraken_reads", "filter_bracken_out", "fix_unmapped", "kreport2krona", "kreport2mpa", "make_kreport", and "make_ktaxonomy".

...

<dynamic dots> Additional arguments passed to kraken_tools command. Empty arguments are automatically trimmed. If a single argument, such as a file path, contains spaces, it must be quoted, for example using shQuote(). Details see: cmd_help(kraken_tools()).

python

A string of path to python command.

Value

A command object.

See also

• https://github.com/jenniferlu717/KrakenTools

• cmd_wd()/cmd_envvar()/cmd_envpath()/cmd_condaenv()

• cmd_on_start()/cmd_on_exit()

• cmd_on_succeed()/cmd_on_fail()

• cmd_parallel()

Other commands: allele_counter(), bcftools(), bedtools(), bowtie2(), bwa(), cellranger(), conda(), fastp(), fastq_pair(), gistic2(), kraken2(), perl(), pyscenic(), python(), samtools(), seqkit(), snpEff(), trust4(), varscan()