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Package: ea-utils (1.1.2+dfsg-5build1)

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

  • depends
  • recommends
  • suggests
  • dep: libc6 (>= 2.29)
    GNU C Library: Shared libraries
    also a virtual package provided by libc6-udeb
  • dep: libgcc-s1 (>= 3.0) [amd64]
    GCC support library
    dep: libgcc-s1 (>= 3.5) [armhf]
  • dep: libgsl23 (>= 2.5)
    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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Architecture Package Size Installed Size Files
amd64 223.2 kB754 kB [list of files]
armhf 150.1 kB411 kB [list of files]