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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).

pirs 2.0.2+dfsg-8

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One-liner (summary)

Profile based Illumina pair-end Reads Simulator

Description

The program pIRS can be used for simulating Illumina PE reads, with a series of characters generated by Illumina sequencing platform, such as insert size distribution, sequencing error(substitution, insertion, deletion), quality score and GC content-coverage bias.

The insert size follows a normal distribution, so users should set the mean value and standard deviation. Usually the standard deviation is set as 1/20 of the mean value. The normal distribution by Box-Muller method is simulated.

The program simulates sequencing error, quality score and GC content- coverage bias according to the empirical distribution profile. Some default profiles counted from lots of real sequencing data are provided.

To simulate reads from diploid genome, users should simulate the diploid genome sequence firstly by setting the ratio of heterozygosis SNP, heterozygosis InDel and structure variation.

License

Unknown

Size

101.6 KB

Downloads

Status	Completed
Checksum (MD5)	eb8069aa34f7a25d1159f2ea987a8e0b
Checksum (SHA-1)	cbae61ec75738916aedfafc9cab4d3dc788ba6fc
Checksum (SHA-256)	e54142ce7c9e049679a14fd83240472a19f85f41f8ef2413b830902964beb573
Checksum (SHA-512)	819805a169fe38a7358f680a6fe4cfd74c94c38493a5659f8b33982a0a440eb821…
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	6 months, 3 weeks ago
Uploaded By
Slug Id	pirs_202dfsg-8_arm64deb-ckui
Unique Id	dNHCyDXET7Hm
Version (Raw)	2.0.2+dfsg-8
Version (Parsed)	Major: 2 Minor: 0 Patch: 2 Type: SemVer (Strict) Metadata: dfsg-8
	extended metadata
Homepage	https://github.com/galaxy001/pirs
Installed Size	351.0 KB
Maintainer	Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Priority	optional
Section	science

Dependencies

Checksum (md5)

f17889a84ef4ffd26860f0b62b643643

Depends	fonts-liberation
Depends	gnuplot
Depends	libc6	>=2.17
Depends	libgcc1	>=1:3.0
Depends	libgomp1	>=4.9
Depends	libgzstream0	>=1.5+dfsg
Depends	libstdc++6	>=5.2
Depends	pirs-profiles
Depends	zlib1g	>=1:1.2.0.2

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[![This version of 'pirs' @ Cloudsmith](https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/pirs/2.0.2+dfsg-8/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true)](https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/pirs/2.0.2+dfsg-8/a=arm64;xc=main;d=debian%252Fbuster;t=binary/)

|This version of 'pirs' @ Cloudsmith|
.. |This version of 'pirs' @ Cloudsmith| image:: https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/pirs/2.0.2+dfsg-8/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true
   :target: https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/pirs/2.0.2+dfsg-8/a=arm64;xc=main;d=debian%252Fbuster;t=binary/

image::https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/pirs/2.0.2+dfsg-8/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true[link="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/pirs/2.0.2+dfsg-8/a=arm64;xc=main;d=debian%252Fbuster;t=binary/",title="This version of 'pirs' @ Cloudsmith"]

<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/pirs/2.0.2+dfsg-8/a=arm64;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/pirs/2.0.2+dfsg-8/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true" alt="This version of 'pirs' @ Cloudsmith" /></a>

rendered as:

To embed the badge for the latest package version, use the following:

[![Latest version of 'pirs' @ Cloudsmith](https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/pirs/latest/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true)](https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/pirs/latest/a=arm64;xc=main;d=debian%252Fbuster;t=binary/)

|Latest version of 'pirs' @ Cloudsmith|
.. |Latest version of 'pirs' @ Cloudsmith| image:: https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/pirs/latest/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true
   :target: https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/pirs/latest/a=arm64;xc=main;d=debian%252Fbuster;t=binary/

image::https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/pirs/latest/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true[link="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/pirs/latest/a=arm64;xc=main;d=debian%252Fbuster;t=binary/",title="Latest version of 'pirs' @ Cloudsmith"]

<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/pirs/latest/a=arm64;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/pirs/latest/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true" alt="Latest version of 'pirs' @ Cloudsmith" /></a>

rendered as:

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

To install/use pirs @ version 2.0.2+dfsg-8 ...

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 pirs=2.0.2+dfsg-8

Warning: Note that this package is for Debian 10 (Buster) / arm64 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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