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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).

Debian logo reapr  1.0.18+dfsg-4

One-liner (summary)

universal tool for genome assembly evaluation

Description

REAPR is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an assembly for manual inspection. It reports mis-assemblies and other warnings, and produces a new broken assembly based on the error calls.

The software requires as input an assembly in FASTA format and paired reads mapped to the assembly in a BAM file. Mapping information such as the fragment coverage and insert size distribution is analysed to locate mis-assemblies. REAPR works best using mapped read pairs from a large insert library (at least 1000bp). Additionally, if a short insert Illumina library is also available, REAPR can combine this with the large insert library in order to score each base of the assembly.

License

Unknown

Size

167.6 KB

Downloads

1

Status  Completed
Checksum (MD5) 3145752685b5671133da2839c82b2ebc
Checksum (SHA-1) d4fed19252156ead2a66e3c6cb88093a75836133
Checksum (SHA-256) 3fa2891cd0a95c78cf44afdc9f327e9face4b97233b820749a91805b6ab38f5a
Checksum (SHA-512) 01154c71b18f2d8f3c9eefc7df5a11c491bfd2cc4de61a2e4436b019078a50d90e…
GPG Signature
GPG Fingerprint c0a114330029b468b1146f70c334efcb2c4f9be3
Distribution debian/buster - Debian - 10 (Buster)
Storage Region  Dublin, Ireland
Type  Binary (contains binaries and binary artifacts)
Uploaded At 11 months ago
Uploaded By alex-borro
Slug Id reapr_1018dfsg-4_armhfdeb-txtm
Unique Id zjn0Z7FNIk9s
Version (Raw) 1.0.18+dfsg-4
Version (Parsed)
  • Major: 1
  • Minor: 0
  • Patch: 18
  • Type: SemVer (Strict)
  • Metadata: dfsg-4
  extended metadata
Homepage http://www.sanger.ac.uk/science/tools/reapr
Installed Size 639.0 KB
Maintainer Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Priority optional
Section science
pkg reapr_1.0.18+dfsg-4_armhf.deb 1
167.6 KB
md5 sha1 sha256 sha512
Package Contents (reapr_1.0.18+dfsg-4_armhf.deb)
Loading...

This package has 52 files/directories.

Dependencies

14

Checksum (md5)

8f2e5b755a8668ca923c7bd4d5c0ee65

Depends
bamtools
Depends
libbamtools2.5.1
Depends
libc6 >=2.4
Depends
libfile-copy-link-perl
Depends
libgcc1 >=1:3.5
Depends
libhts2 >=1.0
Depends
libstdc++6 >=5.2
Depends
libtabixpp0
Depends
r-base
Depends
samtools >=1.3
Depends
smalt
Depends
snpomatic
Depends
tabix
Depends
zlib1g >=1:1.1.4

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|This version of 'reapr' @ Cloudsmith|
.. |This version of 'reapr' @ Cloudsmith| image:: https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/reapr/1.0.18+dfsg-4/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true
   :target: https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/reapr/1.0.18+dfsg-4/a=armhf;xc=main;d=debian%252Fbuster;t=binary/
image::https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/reapr/1.0.18+dfsg-4/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true[link="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/reapr/1.0.18+dfsg-4/a=armhf;xc=main;d=debian%252Fbuster;t=binary/",title="This version of 'reapr' @ Cloudsmith"]
<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/reapr/1.0.18+dfsg-4/a=armhf;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/reapr/1.0.18+dfsg-4/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true" alt="This version of 'reapr' @ Cloudsmith" /></a>

rendered as: This version of 'reapr' @ Cloudsmith

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

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

rendered as: Latest version of 'reapr' @ Cloudsmith

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

To install/use reapr @ version 1.0.18+dfsg-4 ...

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 reapr=1.0.18+dfsg-4
Warning: Note that this package is for Debian 10 (Buster) / armhf and may only work for that configuration.
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