---
name: "needle-ibf"
section: "1"
platform: "linux"
package: "seqan-needle"
version: "1.0.3+ds-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/needle-ibf"
---

# needle-ibf(1)

Constructs the Needle index.

## 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**.