---
name: "needle"
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"
---

# needle(1)

## NAME

needle -

## DESCRIPTION

Needle allows you to build an Interleaved Bloom Filter (IBF) with the command ibf or estimate the expression of transcripts with the command estimate.

## SUBCOMMANDS

This program must be invoked with one of the following subcommands:\
 \- **count**\
 \- **delete**\
 \- **estimate**\
 \- **genome**\
 \- **ibf**\
 \- **ibfmin**\
 \- **insert**\
 \- **insertmin**\
 \- **minimiser**

See the respective help page for further details (e.g. by calling needle count -h).

The following options below belong to the top-level parser and need to be specified **before** the subcommand key word. Every argument after the subcommand key word is passed on to the corresponding sub-parser.

## 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 \[html, man\].

## VERSION

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

## URL

https://github.com/seqan/needle

## LEGAL

**needle 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**.