Source: ea-utils Maintainer: Debian Med Packaging Team Uploaders: Tim Booth , Andreas Tille Section: science Priority: optional Build-Depends: debhelper-compat (= 13), libbam-dev, zlib1g-dev, libgsl-dev, libsparsehash-dev, r-cran-hmisc Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/ea-utils Vcs-Git: https://salsa.debian.org/med-team/ea-utils.git Homepage: https://expressionanalysis.github.io/ea-utils/ Rules-Requires-Root: no Package: ea-utils Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, r-base-core, r-cran-getopt, r-cran-hmisc, r-cran-lattice, r-cran-survival, r-cran-formula, r-cran-ggplot2 Recommends: med-config (>= 2.1) Description: 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.