Man page - needle-ibf(1)

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Manual

NEEDLE-IBF

NAME
POSITIONAL ARGUMENTS
OPTIONS
Basic options:
VERSION
URL
LEGAL

NAME

needle-ibf - Constructs the Needle index.

POSITIONAL ARGUMENTS

ARGUMENT-1 ( List of std::filesystem::path )

Please provide at least one sequence file OR provide one file containing all sequence files with the extension ’.lst’. Default: [].

OPTIONS

Basic 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].

-k , --kmer ( unsigned 8 bit integer )

Define k-mer size for the minimisers. Default: 20. Default: 20.

-w , --window ( unsigned 32 bit integer )

Define window size for the minimisers. Default: 60. Default: 0.

--shape ( unsigned 64 bit integer )

Define a shape for the minimisers by the decimal of a bitvector, where 0 symbolizes a position to be ignored, 1 a position considered. Default: ungapped. Default: 0.

--seed ( unsigned 64 bit integer )

Define seed for the minimisers. Default: 0.

-o , --out ( std::filesystem::path )

Directory, where output files should be saved. Default: "./".

-t , --threads ( unsigned 8 bit integer )

Number of threads to use. Default: 1. Default: 1.

-c , --compressed

If c is set, the IBFS are compressed. Default: Not compressed.

-f , --fpr ( List of double )

List of bin false positive rate per expression level. If only one is given, then that fpr is used for all expression levels. Default: [].

-e , --expression_thresholds ( List of unsigned 16 bit integer )

Which expression thresholds should be used for constructing the IBFs. Default: [].

-l , --number_expression_thresholds ( unsigned 8 bit integer )

Number of expression thresholds. Can be set alternatively to expression_thresholds, then the expression thresholds are determined automatically. Default: 0.

-n , --hash ( unsigned 64 bit integer )

Number of hash functions that should be used when constructing one IBF. Default: 1.

--include ( std::filesystem::path )

Sequence file containing minimizers, only those minimizers will be considered. Default: "".

--exclude ( std::filesystem::path )

Sequence file containing minimizers that should not be stored. Default: "".

--samples ( List of signed 32 bit integer )

Define which samples belong together, sum has to be equal to number of sequence files. Default: Every sequence file is one sample from one experiment. Default: [].

-p , --paired

If set, experiments are paired. Default: Not paired.

--cutoff ( List of unsigned 8 bit integer )

Define for each sample, what number of found minimisers should be considered the result of a sequencing error and therefore be ignored. Default: Every sample has anautomatically generated cutoff, which is based on the file size. Default: [].

--experiment-names ( bool )

If set, names of the experiments are stored in a txt file. Default: 0.

--levels-by-genome ( std::filesystem::path )

Sequence file containing minimizers, only those minimizers will be considered for determining the expression thresholds. Default: "".

--ram

If ram is set and multiple threads are used, the multithreading is more RAM friendly at the cost of being slower.

VERSION

Last update: 2024-11-07
needle-ibf version: 1.0.3
SeqAn version: 3.3.0

URL

https://github.com/seqan/needle

LEGAL

needle-ibf Copyright: BSD 3-Clause License
Author: Mitra Darvish
SeqAn Copyright: 2006-2023 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.
In your academic works please cite: Needle: a fast and space-efficient prefilter for estimating the quantification of very large collections of expression experiments; Mitra Darvish, Enrico Seiler, Svenja Mehringer, René Rahn, and Knut Reinert; Bioinformatics, Volume 38, Issue 17, 1 September 2022, Pages 4100-4108. doi: https://doi.org/10.1093/bioinformatics/btac492
For full copyright and/or warranty information see --copyright .