Pakket: ea-utils (1.1.2+dfsg-6)

[ 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.

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• dep: libgcc-s1 (>= 3.5)

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• dep: libgsl25 (>= 2.6)

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• dep: libstdc++6 (>= 5.2)

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• dep: r-base-core

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• dep: zlib1g (>= 1:1.2.3.3)

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• rec: med-config (>= 2.1)

  Debian Med general config package

ea-utils downloaden

Pakket downloaden voor alle beschikbare platforms

Platform	Pakketgrootte	Geïnstalleerde grootte	Bestanden
armhf	146,2 kB	417,0 kB	[overzicht]