raptor-build1

General options

--input (std::filesystem::path)

A layout file from raptor layout, or a file containing file names. The file must contain at least one file path per line, with multiple paths being separated by a whitespace. Each line in the file corresponds to one bin. Valid extensions for the paths in the file are [minimiser] when using preprocessed input from raptor prepare, and [embl,fasta,fa,fna,ffn,faa,frn,fas,fastq,fq,genbank,gb,gbk,sam], possibly followed by [bz2,gz,bgzf]. The input file must exist and read permissions must be granted.

--output (std::filesystem::path)

A valid path for the output file. Write permissions must be granted.

--threads (unsigned 8 bit integer)

The number of threads to use. Default: 1. Value must be a positive integer.

--quiet

Do not print time and memory usage.

k-mer options

--kmer (unsigned 8 bit integer)

The k-mer size. Default: 20, or read from layout file. Value must be in range [1,32].

--window (unsigned 32 bit integer)

The window size. Default: k-mer size. Value must be a positive integer.

--shape (std::string)

The shape to use for k-mers. Mutually exclusive with --kmer. Parsed from right to left. Default: 11111111111111111111 (a k-mer of size 20), or read from layout file. Value must match the pattern '[01]+'.

Index options

--fpr (double)

The false positive rate. Default: 0.050000, or read from layout file. Value must be in range [0.000000,1.000000].

--hash (unsigned 64 bit integer)

The number of hash functions to use. Default: 2, or read from layout file. Value must be in range [1,5].

--parts (unsigned 8 bit integer)

Splits the index in this many parts. Not available for the HIBF. Default: 1. Value must be a power of two.

--compressed

Build a compressed index.

Common options

-h, --help

Prints the help page.

-hh, --advanced-help

Prints the help page including advanced options.

--version

Prints the version information.

--copyright

Prints the copyright/license information.

--export-help (std::string)

Export the help page information. Value must be one of [html, man, ctd, cwl].