| Type: | Package |
| Title: | ACE File to FASTQ Converter |
| Version: | 0.6.0 |
| Description: | 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. |
| Imports: | stringr |
| License: | GPL-3 |
| Encoding: | UTF-8 |
| LazyData: | true |
| RoxygenNote: | 6.1.1 |
| Suggests: | testthat, knitr, rmarkdown, covr |
| VignetteBuilder: | knitr |
| URL: | https://github.com/c5sire/ace2fastq |
| BugReports: | https://github.com/c5sire/ace2fastq/issues |
| NeedsCompilation: | no |
| Packaged: | 2019-06-19 23:38:38 UTC; Reinhard |
| Author: | Reinhard Simon 
[aut, cre] |
| Maintainer: | Reinhard Simon <rsimon64@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2019-06-20 14:50:18 UTC |
ace2fastq
Description
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.
ace2fastq functionality
See: ace_to_fastq
ace_to_fastq
Description
Converts one or more contig sequences in .ace file format to .fastq format. The parameter target_dir has a special value 'stdout' which will just return the contigs as a list.
Usage
ace_to_fastq(filename, target_dir = dirname(filename), name2id = TRUE)
Arguments
filename |
.ace file |
target_dir |
target directory or stdout |
name2id |
use the file name as primary id or not. Default is TRUE. |
Value
list
Author(s)
Reinhard Simon
Examples
library(ace2fastq)
filename <- system.file("sampledat/1.seq.ace", package = "ace2fastq")
fileout <- ace_to_fastq(filename, target_dir = tempdir())
print.ace2fastq
Description
print method for an object of class ace2fastq
Usage
## S3 method for class 'ace2fastq'
print(x, ...)
Arguments
x |
an ace2fastq object |
... |
other print parameters |
Author(s)
Reinhard Simon