Pakket: ea-utils (1.1.2+dfsg-9 en anderen)

[ Bron: ea-utils  ]

command-line tools for processing biological sequencing data

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.

Andere aan ea-utils gerelateerde pakketten

• dep: libc6 (>= 2.34)

  GNU C Bibliotheek: Gedeelde bibliotheken
  Ook een virtueel pakket geboden door: libc6-udeb

• dep: libgcc-s1 (>= 3.0) [niet armel, armhf, i386, mipsel]

  GCC support bibliotheek

  dep: libgcc-s1 (>= 3.5) [armel, armhf]

  dep: libgcc-s1 (>= 4.2) [i386, mipsel]

• dep: libgsl27 (>= 2.7.1)

  GNU Scientific Library (GSL) -- library package

• dep: libstdc++6 (>= 11)

  GNU Standard C++ Library v3

• dep: r-base-core

  GNU R core of statistical computation and graphics system

• dep: r-cran-formula

  GNU R package for extended model formulas

• dep: r-cran-getopt

  GNU R package providing command-line parsing functionality

• dep: r-cran-ggplot2

  implementation of the Grammar of Graphics

• dep: r-cran-hmisc

  GNU R miscellaneous functions by Frank Harrell

• dep: r-cran-lattice

  GNU R package for 'Trellis' graphics

• dep: r-cran-survival

  GNU R package for survival analysis

• dep: zlib1g (>= 1:1.2.3.3)

  compressiebibliotheek - programma's

• rec: med-config (>= 2.1)

  Debian Med general config package

ea-utils downloaden

Pakket downloaden voor alle beschikbare platforms

Platform	Versie	Pakketgrootte	Geïnstalleerde grootte	Bestanden
amd64	1.1.2+dfsg-9+b2	230,6 kB	747,0 kB	[overzicht]
arm64	1.1.2+dfsg-9+b2	208,9 kB	1.003,0 kB	[overzicht]
armel	1.1.2+dfsg-9+b2	208,8 kB	996,0 kB	[overzicht]
armhf	1.1.2+dfsg-9+b2	205,7 kB	740,0 kB	[overzicht]
i386	1.1.2+dfsg-9+b2	242,5 kB	760,0 kB	[overzicht]
mips64el	1.1.2+dfsg-9+b2	229,8 kB	1.094,0 kB	[overzicht]
mipsel	1.1.2+dfsg-9+b2	233,5 kB	1.084,0 kB	[overzicht]
ppc64el	1.1.2+dfsg-9+b2	241,5 kB	1.323,0 kB	[overzicht]
s390x	1.1.2+dfsg-9+b2	212,0 kB	747,0 kB	[overzicht]