Man page - raptor-search(1)

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Manual

RAPTOR-SEARCH

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
General options
Threshold method options
Dynamic thresholding options
Common options
EXAMPLES
VERSION
URL
LEGAL

NAME

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

SYNOPSIS

raptor search --index <file> --query <file> --output <file> [--threads <number>] [--quiet] [--error <number>|--threshold <number>] [--query_length <number>] [--tau <number>] [--pmax <number>] [--cache-thresholds]

DESCRIPTION

Queries a Raptor index.

OPTIONS

General options

--index ( std::filesystem::path )

Provide a valid path to an index. Parts: Without suffix _0

--query ( std::filesystem::path )

Provide a path to the query file. The input file must exist and read permissions must be granted. Valid file extensions are [embl,fasta,fa,fna,ffn,faa,frn,fas,fastq,fq,genbank,gb,gbk,sam], possibly followed by [bz2,gz,bgzf].

--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.

Threshold method options

If no option is set, --error 0 will be used as default.
Setting --query_length also skips validations associated with the query length, e.g., too long/short queries or a high variance in the query lengths. Notably, queries that are shorter than the window size result in undefined behavior.
--error ( unsigned 8 bit integer )

The number of errors. Mutually exclusive with --threshold. Default: 0. Value must be a positive integer or 0.

--threshold ( double )

Ratio of k-mers that need to be found for a hit to occur. Mutually exclusive with --error. Default: None. Value must be in range [0,1].

--query_length ( unsigned 64 bit integer )

The query length. Only influences the threshold when using --error. Enables skipping of the query length computation for both --error and --threshold. Default: Median of sequence lengths in query file.

Dynamic thresholding options

These option have no effect when using --threshold or k-mer size == window size.
A higher threshold means that less, in the extreme case even false negative, results will be produced.
A lower threshold means that more, possibly false positive, results will be produced.
--tau ( double )

The higher tau, the lower the threshold. Default: 0.9999. Value must be in range [0,1].

--p_max ( double )

The higher p_max, the lower the threshold. Default: 0.15. Value must be in range [0,1].

--cache-thresholds

Stores the computed thresholds with an unique name next to the index. In the next search call using this option, the stored thresholds are re-used. Two files are stored:

threshold_*.bin : Depends on query_length, window, kmer/shape, errors,
and tau.
correction_*.bin : Depends on query_length, window, kmer/shape, p_max,
and fpr.

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 search --index raptor.index --query queries.fastq --output search.output

raptor search --index raptor.index --query queries.fastq --output search.output --threshold 0.7

raptor search --index raptor.index --query queries.fastq --output search.output --error 2

raptor search --index raptor.index --query queries.fastq --output search.output --error 2 --query_length 250

VERSION

Last update: Unavailable
Raptor-search 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-search 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 .