Man page - raptor-build(1)

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Manual

RAPTOR-BUILD

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
General options
k-mer options
Index options
Common options
EXAMPLES
VERSION
URL
LEGAL

NAME

Raptor-build - A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.

SYNOPSIS

raptor build --input <file> --output <file> [--threads <number>] [--quiet] [--kmer <number>|--shape <01-pattern>] [--window <number>] [--fpr <number>] [--hash <number>] [--parts <number>] [--compressed]

DESCRIPTION

Constructs a Raptor index.

The input may be a layout file from raptor layout , a list of minimiser files produced from raptor prepare , or a file with a list of files to process.

OPTIONS

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].

EXAMPLES

raptor build --input bins.list --kmer 19 --window 23 --fpr 0.05 --output raptor.index

raptor build --input bins.list --shape 11011 --window 8 --output raptor.index

raptor build --input bins.list --kmer 32 --window 32 --hash 3 --parts 4 --output raptor.index

raptor build --input minimiser.list --fpr 0.05 --output raptor.index

raptor build --input raptor.layout --output raptor.index

raptor build --input raptor.layout --fpr 0.05 --output raptor.index

VERSION

Last update: Unavailable
Raptor-build version: 3.0.1 (commit unavailable)
Sharg version: 1.1.1
SeqAn version: 3.4.0-rc.3

URL

https://github.com/seqan/raptor

LEGAL

Raptor-build Copyright: BSD 3-Clause License
Author: Enrico Seiler
Contact: enrico.seiler@fu-berlin.de
SeqAn Copyright: 2006-2023 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.
In your academic works please cite: Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences; Enrico Seiler, Svenja Mehringer, Mitra Darvish, Etienne Turc, and Knut Reinert; iScience 2021 24 (7): 102782. doi: https://doi.org/10.1016/j.isci.2021.102782
For full copyright and/or warranty information see --copyright .