fastx-toolkit_0.0.14-6_amd64.deb


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Description

fastx-toolkit - FASTQ/A short nucleotide reads pre-processing tools

Property Value
Distribution Debian 10 (Buster)
Repository Debian Main amd64
Package filename fastx-toolkit_0.0.14-6_amd64.deb
Package name fastx-toolkit
Package version 0.0.14
Package release 6
Package architecture amd64
Package type deb
Category role::program science
Homepage http://hannonlab.cshl.edu/fastx_toolkit/
License -
Maintainer Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Download size 109.80 KB
Installed size 615.00 KB
The FASTX-Toolkit is a collection of command line tools for preprocessing
short nucleotide reads in FASTA and FASTQ formats, usually produced by
Next-Generation sequencing machines. The main processing of such FASTA/FASTQ
files is mapping (aligning) the sequences to reference genomes or other
databases using specialized programs like BWA, Bowtie and many others.
However, it is sometimes more productive to preprocess the FASTA/FASTQ files
before mapping the sequences to the genome—manipulating the sequences to
produce better mapping results. The FASTX-Toolkit tools perform some of these
preprocessing tasks.

Alternatives

Package Version Architecture Repository
fastx-toolkit_0.0.14-6_i386.deb 0.0.14 i386 Debian Main
fastx-toolkit - - -

Requires

Name Value
libc6 >= 2.14
libgcc1 >= 1:3.0
libgd-graph-perl -
libgtextutils0v5 -
libperlio-gzip-perl -
libstdc++6 >= 5.2

Download

Type URL
Mirror ftp.br.debian.org
Binary Package fastx-toolkit_0.0.14-6_amd64.deb
Source Package fastx-toolkit

Install Howto

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

Files

Path
/usr/bin/fasta_clipping_histogram.pl
/usr/bin/fasta_formatter
/usr/bin/fasta_nucleotide_changer
/usr/bin/fastq_masker
/usr/bin/fastq_quality_boxplot_graph.sh
/usr/bin/fastq_quality_converter
/usr/bin/fastq_quality_filter
/usr/bin/fastq_quality_trimmer
/usr/bin/fastq_to_fasta
/usr/bin/fastx_artifacts_filter
/usr/bin/fastx_barcode_splitter.pl
/usr/bin/fastx_clipper
/usr/bin/fastx_collapser
/usr/bin/fastx_nucleotide_distribution_graph.sh
/usr/bin/fastx_nucleotide_distribution_line_graph.sh
/usr/bin/fastx_quality_stats
/usr/bin/fastx_renamer
/usr/bin/fastx_reverse_complement
/usr/bin/fastx_trimmer
/usr/bin/fastx_uncollapser
/usr/share/doc/fastx-toolkit/NEWS.Debian.gz
/usr/share/doc/fastx-toolkit/NEWS.gz
/usr/share/doc/fastx-toolkit/README.Debian
/usr/share/doc/fastx-toolkit/README.gz
/usr/share/doc/fastx-toolkit/README.test
/usr/share/doc/fastx-toolkit/THANKS
/usr/share/doc/fastx-toolkit/changelog.Debian.gz
/usr/share/doc/fastx-toolkit/changelog.gz
/usr/share/doc/fastx-toolkit/copyright
/usr/share/doc/fastx-toolkit/run-unit-test
/usr/share/doc/fastx-toolkit/test-data/Makefile.am
/usr/share/doc/fastx-toolkit/test-data/Makefile.gz
/usr/share/doc/fastx-toolkit/test-data/Makefile.in.gz
/usr/share/doc/fastx-toolkit/test-data/fasta_collapser1.fasta
/usr/share/doc/fastx-toolkit/test-data/fasta_collapser1.out
/usr/share/doc/fastx-toolkit/test-data/fasta_formatter1.fasta.gz
/usr/share/doc/fastx-toolkit/test-data/fasta_formatter1.out.gz
/usr/share/doc/fastx-toolkit/test-data/fasta_formatter2.out.gz
/usr/share/doc/fastx-toolkit/test-data/fasta_nuc_changer1.fasta
/usr/share/doc/fastx-toolkit/test-data/fasta_nuc_changer1.out
/usr/share/doc/fastx-toolkit/test-data/fasta_nuc_changer2.fasta
/usr/share/doc/fastx-toolkit/test-data/fasta_nuc_changer2.out
/usr/share/doc/fastx-toolkit/test-data/fasta_uncollapser1.fasta
/usr/share/doc/fastx-toolkit/test-data/fasta_uncollapser1.out
/usr/share/doc/fastx-toolkit/test-data/fastq_masker.fastq
/usr/share/doc/fastx-toolkit/test-data/fastq_masker.out
/usr/share/doc/fastx-toolkit/test-data/fastq_qual_conv1.fastq
/usr/share/doc/fastx-toolkit/test-data/fastq_qual_conv1.out
/usr/share/doc/fastx-toolkit/test-data/fastq_qual_conv1a.out
/usr/share/doc/fastx-toolkit/test-data/fastq_qual_conv2.fastq
/usr/share/doc/fastx-toolkit/test-data/fastq_qual_conv2.out
/usr/share/doc/fastx-toolkit/test-data/fastq_qual_conv2n.out
/usr/share/doc/fastx-toolkit/test-data/fastq_qual_filter1.fastq
/usr/share/doc/fastx-toolkit/test-data/fastq_qual_filter1a.out
/usr/share/doc/fastx-toolkit/test-data/fastq_qual_filter1b.out
/usr/share/doc/fastx-toolkit/test-data/fastq_quality_trimmer.fastq
/usr/share/doc/fastx-toolkit/test-data/fastq_quality_trimmer.out
/usr/share/doc/fastx-toolkit/test-data/fastq_stats1.fastq
/usr/share/doc/fastx-toolkit/test-data/fastq_stats1.out
/usr/share/doc/fastx-toolkit/test-data/fastq_to_fasta1.fastq
/usr/share/doc/fastx-toolkit/test-data/fastq_to_fasta1a.out
/usr/share/doc/fastx-toolkit/test-data/fastq_to_fasta1b.out
/usr/share/doc/fastx-toolkit/test-data/fastx_artifacts1.fasta
/usr/share/doc/fastx-toolkit/test-data/fastx_artifacts1.out
/usr/share/doc/fastx-toolkit/test-data/fastx_artifacts2.fastq
/usr/share/doc/fastx-toolkit/test-data/fastx_artifacts2.out
/usr/share/doc/fastx-toolkit/test-data/fastx_barcode_splitter1.fastq
/usr/share/doc/fastx-toolkit/test-data/fastx_barcode_splitter1.out
/usr/share/doc/fastx-toolkit/test-data/fastx_barcode_splitter1.txt
/usr/share/doc/fastx-toolkit/test-data/fastx_clipper1.fastq
/usr/share/doc/fastx-toolkit/test-data/fastx_clipper1a.out
/usr/share/doc/fastx-toolkit/test-data/fastx_renamer1.fastq
/usr/share/doc/fastx-toolkit/test-data/fastx_renamer1.out
/usr/share/doc/fastx-toolkit/test-data/fastx_rev_comp1.fasta
/usr/share/doc/fastx-toolkit/test-data/fastx_rev_comp2.fastq
/usr/share/doc/fastx-toolkit/test-data/fastx_reverse_complement1.out
/usr/share/doc/fastx-toolkit/test-data/fastx_reverse_complement2.out
/usr/share/doc/fastx-toolkit/test-data/fastx_seqid_uncollapse1.out
/usr/share/doc/fastx-toolkit/test-data/fastx_seqid_uncollapse1.psl
/usr/share/doc/fastx-toolkit/test-data/fastx_trimmer1.fasta
/usr/share/doc/fastx-toolkit/test-data/fastx_trimmer1.out
/usr/share/doc/fastx-toolkit/test-data/fastx_trimmer2.fastq
/usr/share/doc/fastx-toolkit/test-data/fastx_trimmer2.out
/usr/share/doc/fastx-toolkit/test-data/fastx_trimmer_from_end1.fasta
/usr/share/doc/fastx-toolkit/test-data/fastx_trimmer_from_end1.out
/usr/share/lintian/overrides/fastx-toolkit
/usr/share/man/man1/fasta_clipping_histogram.pl.1.gz
/usr/share/man/man1/fasta_formatter.1.gz
/usr/share/man/man1/fasta_nucleotide_changer.1.gz
/usr/share/man/man1/fastq_masker.1.gz
/usr/share/man/man1/fastq_quality_boxplot_graph.sh.1.gz
/usr/share/man/man1/fastq_quality_converter.1.gz
/usr/share/man/man1/fastq_quality_filter.1.gz
/usr/share/man/man1/fastq_quality_trimmer.1.gz
/usr/share/man/man1/fastq_to_fasta.1.gz
/usr/share/man/man1/fastx_artifacts_filter.1.gz
/usr/share/man/man1/fastx_barcode_splitter.pl.1.gz
/usr/share/man/man1/fastx_clipper.1.gz
/usr/share/man/man1/fastx_collapser.1.gz
/usr/share/man/man1/fastx_nucleotide_distribution_graph.sh.1.gz
/usr/share/man/man1/fastx_nucleotide_distribution_line_graph.sh.1.gz
/usr/share/man/man1/fastx_quality_stats.1.gz
/usr/share/man/man1/fastx_renamer.1.gz
/usr/share/man/man1/fastx_reverse_complement.1.gz
/usr/share/man/man1/fastx_trimmer.1.gz
/usr/share/man/man1/fastx_uncollapser.1.gz

Changelog

2018-09-23 - Andreas Tille <tille@debian.org>
fastx-toolkit (0.0.14-6) unstable; urgency=medium
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.1
* Override script-with-language-extension
( see https://lists.debian.org/debian-med/2018/06/msg00043.html )
2017-08-25 - Andreas Tille <tille@debian.org>
fastx-toolkit (0.0.14-5) unstable; urgency=low
[ Steffen Moeller ]
* [debian/upstream/metadata] Added references to 
OMICtools, bio.tools, RRID
[ Andreas Tille ]
* Standards-Version: 4.1.0 (no changes needed)
* Exit after usage to make sure gcc-7 will not assume that code falls
through case statement.
Closes: #853396
* d/rules: do not parse d/changelog
* drop autotools Build-Depends and in d/rules since that's redundant
for debhelper 10
2017-06-05 - Nadiya Sitdykova <rovenskasa@gmail.com>
fastx-toolkit (0.0.14-4) unstable; urgency=low
* Team upload.
[ Nadiya Sitdykova ]
* Add autopkgtest test-suite
* Add tests for fastx_quality_stats and fastq_quality_filter
* Fix typos in fastq_quality_filter test
* Additional tests
* Add info about -Q option to help screens for commmands, where 
it's relevant
2016-12-10 - Andreas Tille <tille@debian.org>
fastx-toolkit (0.0.14-3) unstable; urgency=low
[ Steffen Moeller ]
361a318 Added EDAM annotation for fastx-toolkit.
[ Andreas Tille ]
* Make Build reproducible (thanks for the patch to Chris Lamb
<lamby@debian.org>, the change in d/rules to suppress creation
of manpages was reverted)
Closes: #840140
* cme fix dpkg-control
* debhelper 10
* d/watch: version=4
* Git repository converted to default layout
* hardening=+all
2014-01-12 - Charles Plessy <plessy@debian.org>
fastx-toolkit (0.0.14-1) unstable; urgency=low
53f820d New upstream release (Closes: 715887, 715888)
6a99f79 Default source package branch is now ‘debian/unstable’.
5028533 Conforms with the Policy version 3.9.5.
450b05d debian/watch: follow GitHub.
d2de0ee Build-depend on libtool.
ee94435 debian/rules: adapt for building from Git repository.
6d9b972 Document backward-incompatible changes in debian/NEWS.
d0c8ed5 Mangle upstream version number for release candidates.
58a04c9 Document the repository structure in ‘debian/gbp.conf’.
4786502 Build-depend on automake.
2013-07-10 - Charles Plessy <plessy@debian.org>
fastx-toolkit (0.0.13.2-2) unstable; urgency=low
20c23bd debian/control normalised with config-model-edit.
e23d327 Conforms with Policy 3.9.4.
bd520ae Removed obsolete DM-Upload-Allowed field.
ef94fe2 Added upstream metadata.
5303f09 Use normalised VCS URLs.
381489a Refresh autotools files via dh. (Closes: #727377)
2012-05-15 - Charles Plessy <plessy@debian.org>
fastx-toolkit (0.0.13.2-1) unstable; urgency=low
1313f16 Imported Upstream version 0.0.13.2
dbfb3ae Removed debian/patches/gcc-4.7.patch, applied upstream.
182cd30 Include 7 digits of the commit ID in the changelog entry.
2ae7b63 Spellchecked common “See also” section of the manpages.
363856c Verbose Debhelper.
2012-04-25 - Andreas Tille <tille@debian.org>
fastx-toolkit (0.0.13.1-2) unstable; urgency=low
* debian/control:
- Added myself to Uploaders
- Standards-Version: 3.9.3 (no changes needed)
- Add missing dependencies of Perl scripts
- Add Build-Depends help2man
- Add Perl modules also ad Build-Depends to enable also
running help2man on Perl scripts
* debian/patches/gcc-4.7.patch: Fix build issue with gcc-4.7
Closes: #667161
* debian/rules:
- convert from cdbs to dh to finally enable hardening flags
- use help2man to creat manpages where possible
* debhelper 9 (control+compat) to support hardening flags
* debian/README.Debian: Add hint for useful web page

See Also

Package Description
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fatcat_1.0.5-1_amd64.deb FAT filesystem explore, extract, repair, and forensic tool
fathom_1.0+git.20190120.0439ca-1_amd64.deb Command-line for probing Syzygy tablebases
fatrace_0.13-2_amd64.deb report system wide file access events
fatresize_1.0.2-11_amd64.deb FAT16/FAT32 filesystem resizer
fatsort_1.3.365-1+b1_amd64.deb utility for sorting FAT directory structures
faucc_20180503-1_amd64.deb C compiler generating Intel code for 16bit/32bit CPUs
fauhdlc_20180504-2_amd64.deb experimental VHDL compiler and interpreter
faumachine-data_20180503-4_all.deb Virtual machine running in user mode -- data files
faumachine_20180503-4_amd64.deb Virtual machine running in user mode
faust-common_2.14.4~repack2-1_all.deb functional programming language for realtime audio applications - common files
faust_2.14.4~repack2-1_amd64.deb functional programming language for realtime audio applications
faustworks_0.5~repack0-6_amd64.deb IDE for Faust dsp programming language
fb-music-high_0.1.2+nmu1_all.deb High quality, large music files for Frozen-Bubble
fbautostart_2.718281828-1+b2_amd64.deb XDG compliant autostarting app for Fluxbox
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