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Open-Source — ultimaker (Ultimaker) / debian-backup — Project

A certifiably-awesome open-source package repository curated by Ultimaker, hosted by Cloudsmith.

Note: Packages in this repository are licensed as GNU General Public License v3.0 or later (dependencies may be licensed differently).

bowtie2-examples 2.3.4.3-1

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One-liner (summary)

Examples for bowtie2

Description

An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.

Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes

This package provides some example data to work with bowtie2.

License

Unknown

Size

9.3 MB

Downloads

Status	Completed
Checksum (MD5)	28ae54fd579cf08ce97a536bf427303f
Checksum (SHA-1)	c3d8f604397d85cd64a3a9774a7986c178a2c618
Checksum (SHA-256)	50a6774af1fbf565238a1cd922265a2677fd52a57dff8d8b736d4f298711fb48
Checksum (SHA-512)	024e0c52b92887184cb9905ad029e3283e5a27c72f96204733cf46c03f1620d2d7…
GPG Signature	Download
GPG Fingerprint	c0a114330029b468b1146f70c334efcb2c4f9be3
Distribution	debian/buster - Debian - 10 (Buster)
Storage Region	Dublin, Ireland
Type	Binary (contains binaries and binary artifacts)
Uploaded At	9 months, 3 weeks ago
Uploaded By
Slug Id	bowtie2-examples_2343-1_alldeb-rqaz
Unique Id	2tvgXFHIva1m
Version (Raw)	2.3.4.3-1
Version (Parsed)	Major: 2 Minor: 3 Patch: 4 Rev1: 3 Pre (Str): (empty) Pre (Num Array): 1 Type: SemVer (Compat)
	extended metadata
Homepage	http://bowtie-bio.sourceforge.net/bowtie2
Installed Size	9.4 MB
Maintainer	Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Priority	optional
Section	science
Source	bowtie2

Dependencies

Checksum (md5)

3f783bdf7a7e224f5b87e1004fec78ae

Recommends	bowtie2
Enhances	bowtie2

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[![This version of 'bowtie2-examples' @ Cloudsmith](https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/bowtie2-examples/2.3.4.3-1/a=all;xc=main;d=debian%252Fbuster;t=binary/?render=true)](https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/bowtie2-examples/2.3.4.3-1/a=all;xc=main;d=debian%252Fbuster;t=binary/)

|This version of 'bowtie2-examples' @ Cloudsmith|
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image::https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/bowtie2-examples/2.3.4.3-1/a=all;xc=main;d=debian%252Fbuster;t=binary/?render=true[link="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/bowtie2-examples/2.3.4.3-1/a=all;xc=main;d=debian%252Fbuster;t=binary/",title="This version of 'bowtie2-examples' @ Cloudsmith"]

<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/bowtie2-examples/2.3.4.3-1/a=all;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/bowtie2-examples/2.3.4.3-1/a=all;xc=main;d=debian%252Fbuster;t=binary/?render=true" alt="This version of 'bowtie2-examples' @ Cloudsmith" /></a>

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|Latest version of 'bowtie2-examples' @ Cloudsmith|
.. |Latest version of 'bowtie2-examples' @ Cloudsmith| image:: https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/bowtie2-examples/latest/a=all;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true
   :target: https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/bowtie2-examples/latest/a=all;xc=main;d=debian%252Fbuster;t=binary/

image::https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/bowtie2-examples/latest/a=all;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true[link="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/bowtie2-examples/latest/a=all;xc=main;d=debian%252Fbuster;t=binary/",title="Latest version of 'bowtie2-examples' @ Cloudsmith"]

<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/bowtie2-examples/latest/a=all;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/bowtie2-examples/latest/a=all;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true" alt="Latest version of 'bowtie2-examples' @ Cloudsmith" /></a>

rendered as:

These instructions assume you have setup the repository first (or read it).

To install/use bowtie2-examples @ version 2.3.4.3-1 ...

To install packages, you can quickly setup the repository automatically (recommended):

curl -1sLf \
  'https://dl.cloudsmith.io/public/ultimaker/debian-backup/setup.deb.sh' \
  | sudo -E bash

If you need to force a specific distribution, release/version, architecture, or component (if supported), you can also do that (e.g. if your system is compatible but not identical):

curl -1sLf \
  'https://dl.cloudsmith.io/public/ultimaker/debian-backup/setup.deb.sh' \
  | sudo -E distro=debian codename=buster arch=ARCH component=COMPONENT bash

or ... you can manually configure it yourself before installing packages:

apt-get install -y debian-keyring  # debian only
apt-get install -y debian-archive-keyring  # debian only
apt-get install -y apt-transport-https
# For Debian Stretch, Ubuntu 16.04 and later
keyring_location=/usr/share/keyrings/ultimaker-debian-backup-archive-keyring.gpg
# For Debian Jessie, Ubuntu 15.10 and earlier
keyring_location=/etc/apt/trusted.gpg.d/ultimaker-debian-backup.gpg
curl -1sLf 'https://dl.cloudsmith.io/public/ultimaker/debian-backup/gpg.C334EFCB2C4F9BE3.key' |  gpg --dearmor >> ${keyring_location}
curl -1sLf 'https://dl.cloudsmith.io/public/ultimaker/debian-backup/config.deb.txt?distro=debian&codename=buster&component=main' > /etc/apt/sources.list.d/ultimaker-debian-backup.list
sudo chmod 644 ${keyring_location}
sudo chmod 644 /etc/apt/sources.list.d/ultimaker-debian-backup.list
apt-get update

sudo apt-get install bowtie2-examples=2.3.4.3-1

Warning: Note that this package is for Debian 10 (Buster) / all and may only work for that configuration.

Still stuck? Need help? Don't panic. Just contact us for help (even if you're not a customer).

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