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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).

soapsnp 1.03-3

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One-liner (summary)

resequencing utility that can assemble consensus sequence of genomes

Description

For getting ideas on the cause of diseases or their response to therapy, and for understanding either for a particular patient, doctors around the globe are starting to look at the genes or the whole genome and how that sequence is different from a healthy / well responding individual.

SOAPsnp is a member of the SOAP (Short Oligonucleotide Analysis Package). The program is a resequencing utility. It assembles the consensus sequence for the genome of a newly sequenced individual based on the alignment of the raw sequencing reads on a known reference. SNPs can then be identified on the consensus sequence through the comparison with the reference.

SOAPsnp uses a method based on Bayes' theorem (the reverse probability model) to call consensus genotype by carefully considering the data quality, alignment, and recurring experimental errors. All these kinds of information was integrated into a single quality score for each base in PHRED scale to measure the accuracy of consensus calling. Currently, it supports the alignment format of SOAPaligner (soap2).

License

Unknown

Size

42.0 KB

Downloads

Status	Completed
Checksum (MD5)	35c6f551acfa32c51826437e7a48e8d3
Checksum (SHA-1)	33c9d8eb398404d31e82fee512e71290ada469ac
Checksum (SHA-256)	6b382f4ab9e9d0cbb365787aead250a1e326da1068d5c37ef640049533efd031
Checksum (SHA-512)	14403979a126c1699e146c9099c82cac4c21f8ba8b9470c59b14735e257f4a8123…
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	1 year, 1 month ago
Uploaded By
Slug Id	soapsnp_103-3_arm64deb-nl9g
Unique Id	y1AuNNacH87b
Version (Raw)	1.03-3
Version (Parsed)	Major: 1 Minor: 3 Pre (Str): (empty) Pre (Num Array): 3 Type: SemVer (Compat)
	extended metadata
Homepage	http://soap.genomics.org.cn/soapsnp.html
Installed Size	94.0 KB
Maintainer	Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Priority	optional
Section	science

Dependencies

Checksum (md5)

c0f1de9c8bc71c5eb1b7ab9a3be6f7e8

Depends	libc6	>=2.17
Depends	libgcc1	>=1:3.0
Depends	libstdc++6	>=5.2
Depends	zlib1g	>=1:1.1.4
Suggests	genomics.cn-soapsnp

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

To install/use soapsnp @ version 1.03-3 ...

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 soapsnp=1.03-3

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).

Previous Version: 1.03-3

Next Version: 1.03-3

soapsnp 1.03-3	debian/buster deb armhf main latest 39.0 KB — 1 year, 1 month ago	3
soapsnp 1.03-3	debian/buster deb arm64 main latest 42.0 KB — 1 year, 1 month ago	3
soapsnp 1.03-3	debian/buster deb armhf main latest 39.0 KB — 1 year, 1 month ago	3

soapsnp 1.03-3

One-liner (summary)

Description

License

Size

Downloads

Tags

This package has 11 files/directories.

soapsnp

soapsnp

soapsnp

Dependencies

Checksum (md5)