ACE File to FASTQ Converter

The ACE file format is used in genomics to store contigs from sequencing machines. This tools converts it into FASTQ format. Both formats contain the sequence characters and their corresponding quality information. Unlike the FASTQ file, the ace file stores the quality values numerically. The conversion algorithm uses the standard Sanger formula. The package facilitates insertion into pipelines, and content inspection.

ace2fastq

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"