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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 python3-sqt  0.8.0-3

One-liner (summary)

SeQuencing Tools for biological DNA/RNA high-throughput data

Description

sqt is a collection of command-line tools for working with high-throughput sequencing data. Conceptionally not fixed to use any particular language, many sqt subcommands are currently implemented in Python. For them, a Python package is available with functions for reading and writing FASTA/FASTQ files, computing alignments, quality trimming, etc.

The following tools are offered: * sqt-coverage -- Compute per-reference statistics such as coverage and GC content * sqt-fastqmod -- FASTQ modifications: shorten, subset, reverse complement, quality trimming. * sqt-fastastats -- Compute N50, min/max length, GC content etc. of a FASTA file * sqt-qualityguess -- Guess quality encoding of one or more FASTA files. * sqt-globalalign -- Compute a global or semiglobal alignment of two strings. * sqt-chars -- Count length of the first word given on the command line. * sqt-sam-cscq -- Add the CS and CQ tags to a SAM file with colorspace reads. * sqt-fastamutate -- Add substitutions and indels to sequences in a FASTA file. * sqt-fastaextract -- Efficiently extract one or more regions from an indexed FASTA file. * sqt-translate -- Replace characters in FASTA files (like the 'tr' command). * sqt-sam-fixn -- Replace all non-ACGT characters within reads in a SAM file. * sqt-sam-insertsize -- Mean and standard deviation of paired-end insert sizes. * sqt-sam-set-op -- Set operations (union, intersection, ...) on SAM/BAM files. * sqt-bam-eof -- Check for the End-Of-File marker in compressed BAM files. * sqt-checkfastqpe -- Check whether two FASTQ files contain correctly paired paired-end data.

License

Unknown

Size

110.9 KB

Downloads

0

Status  Completed
Checksum (MD5) c7dda41345734cb964af9b3d1e1bbdbf
Checksum (SHA-1) 77180fa4b27a2417961289ee9f47944009ed2f7d
Checksum (SHA-256) 7a96e173fce579315d4063630b2d4bc09d277aa1ba3a134839d843477ef4545a
Checksum (SHA-512) 1f82e5179c09b7e07df36c2c67d6eac85e8987bdee7cc51de6f2bf101ba5d875f6…
GPG Signature
GPG Fingerprint c0a114330029b468b1146f70c334efcb2c4f9be3
Distribution debian/buster - Debian - 10 (Buster)
Storage Region  Dublin, Ireland
Type  Binary (contains binaries and binary artifacts)
Uploaded At 5 months, 3 weeks ago
Uploaded By alex-borro
Slug Id python3-sqt_080-3_arm64deb-1q1d
Unique Id rDGLIpEdUriY
Version (Raw) 0.8.0-3
Version (Parsed)
  • Major: 0
  • Minor: 8
  • Patch: 0
  • Pre (Str): (empty)
  • Pre (Num Array): 3
  • Type: SemVer (Strict)
  extended metadata
Homepage https://bitbucket.org/marcelm/sqt
Installed Size 400.0 KB
Maintainer Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Priority optional
Section python
Source python-sqt
pkg python3-sqt_0.8.0-3_arm64.deb 0
110.9 KB
md5 sha1 sha256 sha512
Package Contents (python3-sqt_0.8.0-3_arm64.deb)
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This package has 76 files/directories.

Dependencies

10

Checksum (md5)

a2ee8918f7a5f92f423c67ef1313b84c

Depends
libc6 >=2.17
Depends
python3 <<3.8
Depends
python3 >=3.7~
Depends
python3-cutadapt
Depends
python3-matplotlib
Depends
python3-pysam >=0.10
Depends
python3-seaborn
Depends
python3-xopen
Depends
python3:any
Recommends
fonts-noto-color-emoji
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<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/python3-sqt/0.8.0-3/a=arm64;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/python3-sqt/0.8.0-3/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true" alt="This version of 'python3-sqt' @ Cloudsmith" /></a>

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To install/use python3-sqt @ version 0.8.0-3 ...

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 python3-sqt=0.8.0-3
Warning: Note that this package is for Debian 10 (Buster) / arm64 and may only work for that configuration.
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