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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 segemehl  0.3.4-1

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One-liner (summary)

short read mapping with gaps

Description

Segemehl is a software to map short sequencer reads to reference genomes. Segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl accepts fasta and fastq queries (gzip’ed and bgzip'ed). In addition to the alignment of reads from standard DNA- and RNA-seq protocols, it also allows the mapping of bisulfite converted reads (Lister and Cokus) and implements a split read mapping strategy. The output of segemehl is a SAM or BAM formatted alignment file. In the case of split-read mapping, additional BED files are written to the disc. These BED files may be summarized with the postprocessing tool haarz. In the case of the alignment of bisulfite converted reads, raw methylation rates may also be called with haarz.

In brief, for each suffix of a read, segemehl aims to find the best-scoring seed. Seeds might contain insertions, deletions, and mismatches (differences). The number of differences allowed within a single seed is user-controlled and is crucial for the runtime of the program. Subsequently, seeds that undercut the user-defined E-value are passed on to an exact semi-global alignment procedure. Finally, reads with a minimum accuracy of percent are reported to the user.

License

Unknown

Size

246.5 KB

Downloads

0

Tags

debian/buster deb armhf main latest

Status  Completed
Checksum (MD5) 6bd0bb9d9fa51589872a9a4a49d5e325
Checksum (SHA-1) 36f1d5f9c410dff65d073301d0a130ab39b3d0c9
Checksum (SHA-256) 8432ed3986acff62bcf0c416b33183e86d693df4d458f8b72aca2c0e34b17f4a
Checksum (SHA-512) 5afac059ebe07da01861b73f379e9ab5b12bc26c2938b5b31a7b16684a66c42038…
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 5 months, 2 weeks ago
Uploaded By alex-borro
Slug Id segemehl_034-1_armhfdeb-h7dq
Unique Id LKLa80XnYUhh
Version (Raw) 0.3.4-1
Version (Parsed)
  • Major: 0
  • Minor: 3
  • Patch: 4
  • Pre (Str): (empty)
  • Pre (Num Array): 1
  • Type: SemVer (Strict)
  extended metadata
Homepage http://www.bioinf.uni-leipzig.de/Software/segemehl/
Installed Size 793.0 KB
Maintainer Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Priority optional
Section science
pkg segemehl_0.3.4-1_armhf.deb 0
246.5 KB 		md5 sha1 sha256 sha512
Package Contents (segemehl_0.3.4-1_armhf.deb)
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This package has 14 files/directories.

Dependencies

5

Checksum (md5)

95305617685501f7ea2f7af9bfbbb51e

Depends
libc6 >=2.23
Depends
libhts2 >=1.4.1
Depends
libncurses6 >=6
Depends
libtinfo6 >=6
Depends
zlib1g >=1:1.2.2.4
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|This version of 'segemehl' @ Cloudsmith|
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   :target: https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/segemehl/0.3.4-1/a=armhf;xc=main;d=debian%252Fbuster;t=binary/
image::https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/segemehl/0.3.4-1/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true[link="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/segemehl/0.3.4-1/a=armhf;xc=main;d=debian%252Fbuster;t=binary/",title="This version of 'segemehl' @ Cloudsmith"]
<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/segemehl/0.3.4-1/a=armhf;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/segemehl/0.3.4-1/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true" alt="This version of 'segemehl' @ Cloudsmith" /></a>

rendered as: This version of 'segemehl' @ Cloudsmith

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|Latest version of 'segemehl' @ Cloudsmith|
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   :target: https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/segemehl/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/
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rendered as: Latest version of 'segemehl' @ Cloudsmith

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

To install/use segemehl @ version 0.3.4-1 ...

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 segemehl=0.3.4-1
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).
Previous Version: 0.3.4-1
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