RAPTOR-PREPARE(1) RAPTOR-PREPARE(1)

Raptor-prepare - A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.

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

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

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

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.

A valid path for the output directory.
*.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.
The number of threads to use. Default: 1. Value must be a positive integer.
Do not print time and memory usage.

The k-mer size. Default: 20. Value must be in range [1,32].
The window size. Default: k-mer size. Value must be a positive integer.
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]+'.

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].
Apply cutoffs from Mantis(Pandey et al., 2018). Mutually exclusive with --kmer-count-cutoff.

Prints the help page.
Prints the help page including advanced options.
Prints the version information.
Prints the copyright/license information.
Export the help page information. Value must be one of [html, man, ctd, cwl].

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

Last update: Unavailable
Raptor-prepare version: 3.0.1 (commit unavailable)
Sharg version: 1.1.1
SeqAn version: 3.3.0-rc.2

https://github.com/seqan/raptor

Raptor-prepare 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-prepare 3.0.1 (commit unavailable)