.TH RAPTOR-BUILD 1 "Unavailable" "raptor-build 3.0.1 (commit unavailable)" ""
.SH NAME
Raptor-build \- A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.
.SH SYNOPSIS
\fBraptor\fP build --input <file> --output <file> [--threads <number>] [--quiet] [--kmer <number>|--shape <01-pattern>] [--window <number>] [--fpr <number>] [--hash <number>] [--parts <number>] [--compressed]
.SH DESCRIPTION
Constructs a Raptor index.
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The input may be a layout file from \fBraptor layout\fP, a list of minimiser files produced from \fBraptor prepare\fP, or a file with a list of files to process.
.SH OPTIONS
.SS General options
.TP
\fB--input\fP (\fIstd::filesystem::path\fP)
A layout file from \fBraptor layout\fP, 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 \fBraptor prepare\fP, 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.
.TP
\fB--output\fP (\fIstd::filesystem::path\fP)
 A valid path for the output file. Write permissions must be granted.
.TP
\fB--threads\fP (\fIunsigned 8 bit integer\fP)
The number of threads to use. Default: 1. Value must be a positive integer.
.TP
\fB--quiet\fP
Do not print time and memory usage.
.SS k-mer options
.TP
\fB--kmer\fP (\fIunsigned 8 bit integer\fP)
The k-mer size. Default: 20, or read from layout file. Value must be in range [1,32].
.TP
\fB--window\fP (\fIunsigned 32 bit integer\fP)
The window size. Default: k-mer size. Value must be a positive integer.
.TP
\fB--shape\fP (\fIstd::string\fP)
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]+'.
.SS Index options
.TP
\fB--fpr\fP (\fIdouble\fP)
The false positive rate. Default: 0.050000, or read from layout file. Value must be in range [0.000000,1.000000].
.TP
\fB--hash\fP (\fIunsigned 64 bit integer\fP)
The number of hash functions to use. Default: 2, or read from layout file. Value must be in range [1,5].
.TP
\fB--parts\fP (\fIunsigned 8 bit integer\fP)
Splits the index in this many parts. Not available for the HIBF. Default: 1. Value must be a power of two.
.TP
\fB--compressed\fP
Build a compressed index.
.SS Common 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, ctd, cwl].
.SH EXAMPLES
raptor build --input bins.list --kmer 19 --window 23 --fpr 0.05 --output raptor.index
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raptor build --input bins.list --shape 11011 --window 8 --output raptor.index
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raptor build --input bins.list --kmer 32 --window 32 --hash 3 --parts 4 --output raptor.index
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raptor build --input minimiser.list --fpr 0.05 --output raptor.index
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raptor build --input raptor.layout --output raptor.index
.sp
raptor build --input raptor.layout --fpr 0.05 --output raptor.index
.SH VERSION
\fBLast update: \fRUnavailable
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\fBRaptor-build version: \fR3.0.1 (commit unavailable)
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\fBSharg version: \fR1.1.1
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\fBSeqAn version: \fR3.3.0
.SH URL
https://github.com/seqan/raptor
.SH LEGAL
\fBRaptor-build 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: \fR2006-2023 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.