Paket: ea-utils (1.1.2+dfsg-9 och andra) [debports]

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Externa resurser:

Hemsida [expressionanalysis.github.io]

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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.

Andra paket besläktade med ea-utils

beror

rekommenderar

föreslår

enhances

dep: libc6 (>= 2.34)

GNU C-bibliotek: Delade bibliotek
också ett virtuellt paket som tillhandahålls av libc6-udeb
dep: libgcc-s1 (>= 3.4)

GCC stödbibliotek
dep: libgsl27 (>= 2.7.1)

GNU Scientific Library (GSL) -- library package
dep: libstdc++6 (>= 11)

GNU standardbibliotek v3 för C++
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)

Kompressionsbibliotek - körtidspaket

rec: med-config (>= 2.1)

Debian Med general config package

Hämta ea-utils

Hämtningar för alla tillgängliga arkitekturer
Arkitektur	Version	Paketstorlek	Installerad storlek	Filer
riscv64 (inofficiell anpassning)	1.1.2+dfsg-9+b2	217,4 kbyte	617,0 kbyte	[filförteckning]