ea-utils_1.1.2+dfsg-4build1_amd64.deb


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Description

ea-utils - command-line tools for processing biological sequencing data

Property Value
Distribution Ubuntu 18.04 LTS (Bionic Beaver)
Repository Ubuntu Universe amd64
Package name ea-utils
Package version 1.1.2+dfsg
Package release 4build1
Package architecture amd64
Package type deb
Installed size 734 B
Download size 222.30 KB
Official Mirror archive.ubuntu.com
Ea-utils provides a set of command-line tools for processing biological
sequencing data, barcode demultiplexing, adapter trimming, etc.
Primarily written to support an Illumina based pipeline - but should work with
any FASTQs.
Main Tools are:
* fastq-mcf
Scans a sequence file for adapters, and, based on a log-scaled threshold,
determines a set of clipping parameters and performs clipping. Also does
skewing detection and quality filtering.
* fastq-multx
Demultiplexes a fastq. Capable of auto-determining barcode id's based on a
master set fields. Keeps multiple reads in-sync during demultiplexing. Can
verify that the reads are in-sync as well, and fail if they're not.
* fastq-join
Similar to audy's stitch program, but in C, more efficient and supports some
automatic benchmarking and tuning. It uses the same "squared distance for
anchored alignment" as other tools.
* varcall
Takes a pileup and calculates variants in a more easily parameterized manner
than some other tools.

Alternatives

Package Version Architecture Repository
ea-utils_1.1.2+dfsg-4build1_i386.deb 1.1.2+dfsg i386 Ubuntu Universe
ea-utils - - -

Requires

Name Value
libc6 >= 2.15
libgcc1 >= 1:3.0
libgsl23 -
libstdc++6 >= 5.2
r-base-core -
r-cran-formula -
r-cran-getopt -
r-cran-ggplot2 -
r-cran-hmisc -
r-cran-lattice -
r-cran-survival -
zlib1g >= 1:1.2.3.3

Download

Type URL
Binary Package ea-utils_1.1.2+dfsg-4build1_amd64.deb
Source Package ea-utils

Install Howto

  1. Update the package index:
    # sudo apt-get update
  2. Install ea-utils deb package:
    # sudo apt-get install ea-utils

Files

Path
/usr/bin/determine-phred
/usr/bin/ea-alc
/usr/bin/fastq-clipper
/usr/bin/fastq-join
/usr/bin/fastq-mcf
/usr/bin/fastq-multx
/usr/bin/fastq-stats
/usr/bin/fastx-graph
/usr/bin/randomFQ
/usr/bin/sam-stats
/usr/bin/varcall
/usr/lib/debian-med/bin/alc
/usr/lib/debian-med/share/man/man1/alc.1.gz
/usr/share/doc/ea-utils/README.Debian
/usr/share/doc/ea-utils/changelog.Debian.gz
/usr/share/doc/ea-utils/copyright
/usr/share/man/man1/determine-phred.1.gz
/usr/share/man/man1/ea-alc.1.gz
/usr/share/man/man1/fastq-clipper.1.gz
/usr/share/man/man1/fastq-join.1.gz
/usr/share/man/man1/fastq-mcf.1.gz
/usr/share/man/man1/fastq-multx.1.gz
/usr/share/man/man1/fastq-stats.1.gz
/usr/share/man/man1/fastx-graph.1.gz
/usr/share/man/man1/randomFQ.1.gz
/usr/share/man/man1/sam-stats.1.gz
/usr/share/man/man1/varcall.1.gz

Changelog

2017-08-06 - Matthias Klose <doko@ubuntu.com>
ea-utils (1.1.2+dfsg-4build1) artful; urgency=medium
* No-change rebuild for libgsl soname change.
2016-08-02 - Andreas Tille <tille@debian.org>
ea-utils (1.1.2+dfsg-4) unstable; urgency=medium
* New homepage (project moved to Github)
* cme fix dpkg-control
* hardening=+all
* Fix URL in upstream metadata
2015-12-07 - Andreas Tille <tille@debian.org>
ea-utils (1.1.2+dfsg-3) unstable; urgency=medium
* Update build dependencies for GSL 2, change libgsl0-dev to libgsl-dev.
(thanks to Bas Couwenberg for the patch)
Closes: #807198
2015-12-03 - Andreas Tille <tille@debian.org>
ea-utils (1.1.2+dfsg-2) unstable; urgency=medium
* Move /usr/bin/alc to /usr/lib/debian-med/bin/alc
Closes: #794334
2015-07-26 - Andreas Tille <tille@debian.org>
ea-utils (1.1.2+dfsg-1) unstable; urgency=medium
* Initial upload to Debian (Closes: #793585)
2015-01-22 - Tim Booth <tbooth@ceh.ac.uk>
ea-utils (1.1.2-0biolinux4) trusty; urgency=medium
* Re-remove utility copy of sparsehash as v2 is now in the
PPA.
* And don't forget to re-add the dependency
2014-08-19 - Tim Booth <tbooth@ceh.ac.uk>
ea-utils (1.1.2-0biolinux2) trusty; urgency=low
* Initial release for Bio-Linux 8
* Build against samtools from Debian.
* Leave utility copy of sparsehash in for now, as Trusty
has v1 of the lib and we want v2.

See Also

Package Description
eag-healpix-java-doc_2017.09.06-1_all.deb Handling of HEALPix sky pixellization (API docs)
eag-healpix-java_2017.09.06-1_all.deb Handling of HEALPix sky pixellization
eancheck_1.0-2_amd64.deb Check digit validator for EAN/PLU/UPC barcode numbers
earlyoom_1.0-1_amd64.deb Early OOM Daemon
easy-rsa_2.2.2-2_all.deb Simple shell based CA utility
easychem_0.6-8build1_amd64.deb Draw high-quality molecules and 2D chemical formulas
easygit_0.99-2_all.deb git for mere mortals
easyh10_1.5-4_amd64.deb Utility to manage the iRiver H10 music player
easystroke_0.6.0-0ubuntu11_amd64.deb gesture recognition program
easytag-nautilus_2.4.3-4_amd64.deb Nautilus extension for easytag
easytag_2.4.3-4_amd64.deb GTK+ editor for audio file tags
eb-doc_4.4.3-12_all.deb C library for accessing electronic books (documents)
eb-utils_4.4.3-12_amd64.deb C library for accessing electronic books (utilities)
ebhttpd_1.0.dfsg.1-4.3build1_amd64.deb specialized HTTP server to access CD-ROM books
eblook_1.6.1-15_amd64.deb electronic dictionary search command using EB Library
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