An R package to process amplicon data

This package has a number of functions to filter, dereplicate and error and chimera check NGS reads stored in fastq files. From v2.6.0 amplicR implements a function to process paired end reads (data.proc.paired). This functionality has not being implemented in the raw2data.proc wrapper and manual calling of the single functions is needed to carry out the preceding steps in the analytical pipeline. Compatibility of down stream analyses should be preserved, but it has not being. The retained reads after the data processing described above (or your own reads if you have done this already in another way) can then be compared against reference sequences and the number of mismatch is reported. This may be useful when, for example, screening samples for particular taxa (e.g. a pathogen).

amplicR is mainly a wrapper of several functions provided by other R packages in order to automate some common analyses, so if you use it, please make sure to also cite the relevant packages (these are generally indicated in the documentation of amplicR's functions). To find out the correct citation for a package, you can use the function: citation("package_name") where you have to replace package_name with the actual name of the package you are interested into.

Install the package from version control from within R:

library(devtools) 
install_github("carlopacioni/amplicR") 

If you have not used devtools before, then you have to install it with

install.packages("devtools") 

If you are on Windows, before loading devtools, shut down R, download the Rtools executable file from CRAN webpage and run it.

Note that the Bioconductor packages, which are required dependencies for amplicR, are not currently installed along with the package. This may change in the future, but for now these can be installed (if not installed already) running the following:

library(amplicR)
setup()

All reasonable care has been taken to ensure that amplicR functions report the correct results. However there is no guarantee that the package is bug-free. Also, amplicR was developed on a machine running windows 7 and no testing on other OS has been conducted so far. I can't see any reason why it would not work on linux or mac, but if in doubt, you may want to replicate the results on a windows environment.

Use help(amplicR) ?amplicR or ??amplicR to see a broad description of the package. Use help(package = "amplicR") to see the documentations available. Alternatively, a manual is available here and a tutorial is available here.

If you use amplicR, please cite: Pending