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ace2fastq

Project Status: Active – The project has reached a stable, usable state and is being actively developed. Lifecycle: stable AppVeyor build status Travis build status Codecov test coverage

CRAN status Downloads

The package provides a function that converts “.ace” files (ABI Sanger capillary sequence assembly files) to standard “.fastq” files. The file format is currently used in genomics to store contigs. To the best of our knowledge, no R function is available to convert this format into the more popular fastq file format. The development was motivated in the context of the analysis of 16S metagenomic data by the need to convert the .ace files for further analysis.

Installation

You can install the released version of ace2fastq from CRAN with:

install.packages("ace2fastq")

Latest version can be installed from github:

install.packages(devtools)

devtools::install_github("c5sire/ace2fastq")

Example

This is a basic example which shows you how to solve a common problem:

library(ace2fastq)


filename <- system.file("sampledat/1.seq.ace", package = "ace2fastq")

out_file <- ace_to_fastq(filename, target_dir = tempdir())

lines <- readLines(out_file$path)
#> [1] "@1.seq CO Contig1 1489 2 12 U"
#> [1] "gctccctgatgttagcggcggACGGGTGAGTAACACGTGGG"
#> [1] "+"
#> [1] "!!!!!!!!!!!!!!!!!!!!!DUNUUUUUUUNUDIIIUUUU"

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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