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.
kraken2(
fq1,
...,
fq2 = NULL,
ofile = "kraken_output.txt",
report = "kraken_report.txt",
classified_out = NULL,
unclassified_out = NULL,
odir = getwd(),
kraken2 = NULL
)A command object.
A string of fastq file path.
<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()).
A string of path to save kraken2 output.
A string of path to save kraken2 report.
A string of path to save classified sequences, which should be a fastq file.
A string of path to save unclassified sequences, which should be a fastq file.
A string of path to the output directory.
A string of path to kraken2 command.