[ 原始碼： ea-utils ]
套件：ea-utils（1.1.2+dfsg-5）
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-mcfScans 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-multxDemultiplexes 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-joinSimilar 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.
* varcallTakes a pileup and calculates variants in a more easily parameterized manner than some other tools.
其他與 ea-utils 有關的套件
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- dep: libc6 (>= 2.17)
- GNU C 函式庫：共用函式庫
同時作為一個虛擬套件由這些套件填實： libc6-udeb
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- dep: libgcc1 (>= 1:3.0)
- GCC 支援函式庫
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- dep: libgsl23
- GNU Scientific Library (GSL) -- library package
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- dep: libgslcblas0
- GNU Scientific Library (GSL) -- blas library package
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- dep: libstdc++6 (>= 5.2)
- GNU Standard C++ Library v3
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- dep: r-base-core
- GNU R core of statistical computation and graphics system
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- dep: r-cran-formula
- GNU R package for extended model formulas
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- dep: r-cran-getopt
- GNU R package providing command-line parsing functionality
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- dep: r-cran-ggplot2
- implementation of the Grammar of Graphics
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- dep: r-cran-hmisc
- GNU R miscellaneous functions by Frank Harrell
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- dep: r-cran-lattice
- GNU R package for 'Trellis' graphics
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- dep: r-cran-survival
- GNU R package for survival analysis
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- dep: zlib1g (>= 1:1.2.3.3)
- 壓縮函式庫 - 跑程式時用(runtime)
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- rec: med-config (>= 2.1)
- Debian Med general config package