| RAPTOR-BUILD(1) | RAPTOR-BUILD(1) |
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: 3.3.0
URL¶
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.
| Unavailable | raptor-build 3.0.1 (commit unavailable) |