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

[ Source: 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.

Other Packages Related to ea-utils

• dep: libc6 (>= 2.29)

  GNU C Library: Shared libraries
  also a virtual package provided by libc6-udeb

• dep: libgcc-s1 (>= 3.0)

  GCC support library

• dep: libgsl25 (>= 2.6)

  GNU Scientific Library (GSL) -- library package

• dep: libstdc++6 (>= 5.2)

  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)

  compression library - runtime

• rec: med-config (>= 2.1)

  Debian Med general config package

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