.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 POSITIONAL ARGUMENTS
.TP
\fBARGUMENT-1\fP (\fIstd::filesystem::path\fP)
File containing color and 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  preprocessing, and [embl,fasta,fa,fna,ffn,faa,frn,fas,fastq,fq,genbank,gb,gbk,sam], possibly followed by [bz2,gz,bgzf] otherwise.  The input file must exist and read permissions must be granted.
.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--kmer\fP (\fIunsigned 8 bit integer\fP)
The k-mer size. Default: 20. Value must be in range [1,32].
.TP
\fB--output\fP (\fIstd::filesystem::path\fP)
Provide an output filepath. 
.TP
\fB--size\fP (\fIstd::string\fP)
The size in bytes of the resulting index. Default: 1k. Must be an integer followed by [k,m,g,t] (case insensitive).
.TP
\fB--hash\fP (\fIunsigned 64 bit integer\fP)
The number of hash functions to use. Default: 2. Value must be in range [1,5].
.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--compressed\fP
Build a compressed index.
.SH EXAMPLES
raptor build --kmer 19 --window 23 --size 8m --output raptor.index all_bin_paths.txt
.sp
raptor build --kmer 19 --window 23 --compute-minimiser --output precomputed_minimisers all_bin_paths.txt
.sp
raptor build --size 8m --output minimiser_raptor.index all_minimiser_paths.txt
.SH VERSION
\fBLast update: \fR2021-08-20--no-git
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\fBRaptor version: \fR2.0.1 (74f815358db47037e93a56b826a9df3692e55680--no-git)
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\fBSharg version: \fR1.0.0
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\fBSeqAn version: \fR3.2.0
.SH URL
https://github.com/seqan/raptor
.SH LEGAL
\fBRaptor Copyright: \fRBSD 3-Clause License
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\fBAuthor: \fREnrico Seiler
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\fBContact: \fRenrico.seiler@fu-berlin.de
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\fBSeqAn Copyright: \fR2006-2022 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.
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\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
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For full copyright and/or warranty information see \fB--copyright\fR.