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 Open-Source — ultimaker 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).
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Debian logo seqprep  1.3.2-3

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One-liner (summary)

stripping adaptors and/or merging paired reads of DNA sequences with overlap

Description

SeqPrep is a program to merge paired end Illumina reads that are overlapping into a single longer read. It may also just be used for its adapter trimming feature without doing any paired end overlap. When an adapter sequence is present, that means that the two reads must overlap (in most cases) so they are forcefully merged. When reads do not have adapter sequence they must be treated with care when doing the merging, so a much more specific approach is taken. The default parameters were chosen with specificity in mind, so that they could be ran on libraries where very few reads are expected to overlap. It is always safest though to save the overlapping procedure for libraries where you have some prior knowledge that a significant portion of the reads will have some overlap.

License

Unknown

Size

26.5 KB

Downloads

0

Tags

debian/buster deb armhf main latest

Status  Completed
Checksum (MD5) aba3ba14795720d8ae8d27ca0e15bc0d
Checksum (SHA-1) a0944e88a938e30ef2afe5016df110b3b87a6650
Checksum (SHA-256) d45cadf3014cdc0f6ba7738accc06705aaad972f2d6e4ff713145eff72a8e103
Checksum (SHA-512) 435bb100ee68f4c11eb894ab178d0d44da4bf424df05c96c2f06700e13c1ca1a1b…
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 7 months, 3 weeks ago
Uploaded By alex-borro
Slug Id seqprep_132-3_armhfdeb-ipml
Unique Id IXSIBFgxFTUY
Version (Raw) 1.3.2-3
Version (Parsed)
  • Major: 1
  • Minor: 3
  • Patch: 2
  • Pre (Str): (empty)
  • Pre (Num Array): 3
  • Type: SemVer (Strict)
  extended metadata
Homepage http://seqanswers.com/wiki/SeqPrep
Installed Size 90.0 KB
Maintainer Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Priority optional
Section science
pkg seqprep_1.3.2-3_armhf.deb 0
26.5 KB 		md5 sha1 sha256 sha512
Package Contents (seqprep_1.3.2-3_armhf.deb)
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This package has 13 files/directories.

Dependencies

2

Checksum (md5)

301bb78b3a80643c67b5c77f367a94f5

Depends
libc6 >=2.4
Depends
zlib1g >=1:1.1.4
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|This version of 'seqprep' @ Cloudsmith|
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image::https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/seqprep/1.3.2-3/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true[link="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/seqprep/1.3.2-3/a=armhf;xc=main;d=debian%252Fbuster;t=binary/",title="This version of 'seqprep' @ Cloudsmith"]
<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/seqprep/1.3.2-3/a=armhf;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/seqprep/1.3.2-3/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true" alt="This version of 'seqprep' @ Cloudsmith" /></a>

rendered as: This version of 'seqprep' @ Cloudsmith

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[![Latest version of 'seqprep' @ Cloudsmith](https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/seqprep/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/seqprep/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/)
|Latest version of 'seqprep' @ Cloudsmith|
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rendered as: Latest version of 'seqprep' @ Cloudsmith

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

To install/use seqprep @ version 1.3.2-3 ...

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 seqprep=1.3.2-3
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).
Previous Version: 1.3.2-3
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