Paket: ea-utils (1.1.2+dfsg-9 und andere) [debports]

[ Quellcode:  ]

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 Pakete mit Bezug zu ea-utils

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• dep: r-cran-getopt

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• dep: r-cran-ggplot2

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• dep: r-cran-hmisc

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• dep: r-cran-lattice

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• dep: r-cran-survival

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• rec: med-config (>= 2.1)

  Debian Med - allgemeines Konfigurationspaket

ea-utils herunterladen

Download für alle verfügbaren Architekturen

Architektur	Version	Paketgröße	Größe (installiert)	Dateien
ia64 (inoffizielle Portierung)	1.1.2+dfsg-9+b1	300,4 kB	1.332,0 kB	[Liste der Dateien]