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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).

tracetuner 3.0.6~beta+dfsg-1

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One-liner (summary)

interpretation of DNA Sanger sequencing data

Description

Tracetuner is a tool for base and quality calling of trace files from DNA sequencing instruments. Traditional DNA sequencing yields curves from four different channels or light frequencies that human or (preferably) machines are interpreting to determine the actual base (A,C,G or T) and the confidence with which this is determined.

TraceTuner is a DNA sequencing quality value, base calling and trace processing software application originally developed by Paracel, Inc. While providing a flexible interface and capability to adopt the "pure" base calls produced by Phred, KB or any other "original" caller, it offers competitive features not currently available in other tools, such as customized calibration of quality values, advanced heterozygote and mixed base calling and deconvolving the "mixed" electropherograms resulting from the presence of indels into a couple of "pure" electropherograms.

Later versions Previous versions of TraceTuner were used by Celera Genomics to process over 27 million reads from both Drosophila and human genome projects. In 2000, Applied Biosystems bundled TraceTuner with ABI3700 Genome Analyzers and shipped it to the customers of these capillary electrophoresis sequencers. its SNP detection and genotyping software product SeqScape.

TraceTuner implements an advanced peak processing technology for resolving overlapping peaks of the same dye color into individual, or "intrinsic" peaks. TraceTuner, for its support of mixed base calling, have been used by the research community, the private biotech sector, and the U.S. government as components of different variant detection, genotyping and forensic software applications (e.g. Applied Biosystems SeqScape, Paracel Genome Assembler, MTexpert, etc.).

This technology was protected by US Patent #6,681,186. Currently, TraceTuner is an open source software, which has been used by J. Craig Venter Institute's DNA Sequencing and Resequencing pipelines.

This package prepares an important piece of human history to be used with new data on new machines or to revisit older observations..

License

Unknown

Size

303.3 KB

Downloads

Status	Completed
Checksum (MD5)	f5cb1096140c856478a2c51634a1d392
Checksum (SHA-1)	abe6ce606928d00248cfea37e89906f779ce1fc7
Checksum (SHA-256)	c9e0d18a9cb814928b346d1efc3eb1f5fb2e890823c7b756bf90416c4c4a9063
Checksum (SHA-512)	7e39220e61dee0dda777d666f77aac861a32d75fd2aa7967517f72295cd7c67751…
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	tracetuner_306betadfsg-1_armhfdeb-1ouf
Unique Id	3k5XAXdl0CX8
Version (Raw)	3.0.6~beta+dfsg-1
Version (Parsed)	Major: 3 Minor: 0 Patch: 6 Type: SemVer (Compat) Metadata: beta+dfsg-1
	extended metadata
Homepage	https://sourceforge.net/projects/tracetuner/
Installed Size	1.3 MB
Maintainer	Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Priority	optional
Section	science

Dependencies

Checksum (md5)

2130c7b971b5c5aa7554852d85133fc4

Depends	libc6	>=2.7
Depends	libgcc1	>=1:3.5
Depends	zlib1g	>=1:1.1.4

You can embed a badge in another website that shows this or the latest version of this package.

To embed the badge for this specific package version, use the following:

[![This version of 'tracetuner' @ Cloudsmith](https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/tracetuner/3.0.6~beta+dfsg-1/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true)](https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/tracetuner/3.0.6~beta+dfsg-1/a=armhf;xc=main;d=debian%252Fbuster;t=binary/)

|This version of 'tracetuner' @ Cloudsmith|
.. |This version of 'tracetuner' @ Cloudsmith| image:: https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/tracetuner/3.0.6~beta+dfsg-1/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true
   :target: https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/tracetuner/3.0.6~beta+dfsg-1/a=armhf;xc=main;d=debian%252Fbuster;t=binary/

image::https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/tracetuner/3.0.6~beta+dfsg-1/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true[link="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/tracetuner/3.0.6~beta+dfsg-1/a=armhf;xc=main;d=debian%252Fbuster;t=binary/",title="This version of 'tracetuner' @ Cloudsmith"]

<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/tracetuner/3.0.6~beta+dfsg-1/a=armhf;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/tracetuner/3.0.6~beta+dfsg-1/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true" alt="This version of 'tracetuner' @ Cloudsmith" /></a>

rendered as:

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

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

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

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

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

rendered as:

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

To install/use tracetuner @ version 3.0.6~beta+dfsg-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 tracetuner=3.0.6~beta+dfsg-1

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