ea-utils

command-line tools for processing biological sequencing data

Command lineScience

Not tested on a device yet. What that means

Commands in the package

determine-phred
ea-alc
fastq-clipper
fastq-join
fastq-mcf
fastq-multx
fastq-stats
fastx-graph
randomFQ
sam-stats
varcall

About ea-utils

From Debian's package description

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.

From Debian's description of the ea-utils package, under that package's license.

Dependencies

Depends on

libc6
libgcc-s1
libgsl28
libstdc++6
zlib1g
r-base-core
r-cran-getopt
r-cran-hmisc
r-cran-lattice
r-cran-survival
r-cran-formula
r-cran-ggplot2

Recommends

med-config

Related apps

All Linux science apps

Sources and licenses

Name: the Debian package name.
Summary: Debian's short description of the ea-utils package, under that package's license.
Description: Debian's description of the ea-utils package, under that package's license.
Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
Popularity: Debian Popularity Contest counts.