.TH RAPTOR 1 "2021-08-20--no-git" "raptor 2.0.1 (74f815358db47037e93a56b826a9df3692e55680--no-git)" ""
.SH NAME
Raptor \- A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.
.SH OPTIONS
.SS Basic options:
.TP
\fB-h\fP, \fB--help\fP
Prints the help page.
.TP
\fB-hh\fP, \fB--advanced-help\fP
Prints the help page including advanced options.
.TP
\fB--version\fP
Prints the version information.
.TP
\fB--copyright\fP
Prints the copyright/license information.
.TP
\fB--export-help\fP (std::string)
Export the help page information. Value must be one of [html, man].
.TP
\fB--index\fP (\fIstd::filesystem::path\fP)
Provide a valid path to an index. 
.TP
\fB--query\fP (\fIstd::filesystem::path\fP)
Provide a path to the query file. The input file must exist and read permissions must be granted.
.TP
\fB--output\fP (\fIstd::filesystem::path\fP)
Provide a path to the output. 
.TP
\fB--threads\fP (\fIunsigned 8 bit integer\fP)
The numer of threads to use. Default: 1. Value must be a positive integer.
.TP
\fB--cache-thresholds\fP
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:
\fBthreshold_*.bin\fP: Depends on pattern, window, kmer/shape, errors, and tau.
\fBcorrection_*.bin\fP: Depends on pattern, window, kmer/shape, p_max, and fpr.
.SH EXAMPLES
raptor search --error 2 --index raptor.index --query queries.fastq --output search.output
.SH VERSION
\fBLast update: \fR2021-08-20--no-git
.br
\fBRaptor version: \fR2.0.1 (74f815358db47037e93a56b826a9df3692e55680--no-git)
.br
\fBSharg version: \fR1.0.0
.br
\fBSeqAn version: \fR3.2.0
.SH URL
https://github.com/seqan/raptor
.SH LEGAL
\fBRaptor Copyright: \fRBSD 3-Clause License
.br
\fBAuthor: \fREnrico Seiler
.br
\fBContact: \fRenrico.seiler@fu-berlin.de
.br
\fBSeqAn Copyright: \fR2006-2022 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.
.br
\fBIn your academic works please cite: \fRRaptor: 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
.br
For full copyright and/or warranty information see \fB--copyright\fR.