Running Kraken2

Kraken is a taxonomic sequence classifier that assigns taxonomic labels to DNA sequences. Kraken examines the k-mers within a query sequence and uses the information within those k-mers to query a database. That database maps k-mers to the lowest common ancestor (LCA) of all genomes known to contain a given k-mer.

Usage

kraken2(
  reads,
  ...,
  ofile = "kraken_output.txt",
  report = "kraken_report.txt",
  classified_out = NULL,
  unclassified_out = NULL,
  odir = getwd(),
  kraken2 = NULL
)

Arguments

reads

A character vector of FASTQ files used as input to Kraken2. Can be one file (single-end) or two files (paired-end).

...

<dynamic dots> Additional arguments passed to kraken2 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(kraken2()).

ofile

A string of path to save kraken2 output.

report

A string of path to save kraken2 report.

classified_out

A string of path to save classified sequences, which should be a fastq file.

unclassified_out

A string of path to save unclassified sequences, which should be a fastq file.

odir

A string of path to the output directory.

kraken2

A string of path to kraken2 command.

Value

A command object.

See also

• https://github.com/DerrickWood/kraken2/wiki/Manual

• https://benlangmead.github.io/aws-indexes/k2

• 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(), kraken_tools(), perl(), pyscenic(), python(), samtools(), seqkit(), snpEff(), trust4(), varscan()