raptor-prepare(1)

Usage

raptor prepare --input <file> --output <directory> [--threads <number>] [--quiet] [{--kmer <number> | --shape <01-pattern>}] [--window <number>] [{--kmer-count-cutoff <number> | --use-filesize-dependent-cutoff}]

Overview

Computes minimisers for the use with raptor layout and raptor build.

Can continue where it left off after a crash or in multiple runs.

Options

General options

--input (std::filesystem::path): 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 directory.

Will create a minimiser.list inside the output directory. This file contains a list of generated minimiser files, in the same order as the input.

When you manually delete a .in_progress file, also delete the corresponding .header and .minimiser file!

Created output files for each file:

*.header: Contains the shape, window size, cutoff and minimiser count.

*.minimiser: Contains binary minimiser values, one minimiser per line.

*.in_progress: Temporary file to track process. Deleted after finishing computation.

--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. 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). Value must match the pattern '[01]+'.

Processing options

--kmer-count-cutoff (unsigned 8 bit integer): Only store k-mers with at least (>=) x occurrences. Mutually exclusive with --use-filesize-dependent-cutoff. Default: 1. Value must be in range [1,254].

--use-filesize-dependent-cutoff: Apply cutoffs from Mantis(Pandey et al., 2018). Mutually exclusive with --kmer-count-cutoff.

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 prepare --input bins.list --output some_directory --kmer 20 --window 24

raptor prepare --input bins.list --output some_directory --kmer-count-cutoff 2

raptor prepare --input bins.list --output some_directory --use-filesize-dependent-cutoff

Version

Last update: Unavailable
Raptor-prepare 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-prepare Copyright: BSD 3-Clause License
Author: Enrico Seiler
Contact: [email protected]
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.