rDnaTools is a python package of tools and pipelines for working with ribosomal DNA sequence data generated with the PacBio(R) SMRT sequencing. rDnaTools works by wrapping existing tools from microbial ecology, primarily the Mothur suite of utilities.
Currently rDnaTools implements a single pipeline for the export, filtering, and cluster of 16S sequences. Future releases will include automated pipelines for other use-cases, as well as the capability for users to script their own pipelines for rDNA sequence analysis.
Though primarily intended for use in analyzing 16S rDNA sequences, the same tools and approaches should apply equally well to 18S, 23S, or ITS sequences, provided that suitable reference sequences are supplied.
The core functionality of rDnaTools is built upon Python2.7 using the pbcore framework for accessing PacBio data files. In addition rDnaTools wraps the functionality from a number of stand-alone commandline tools that must available for the package to function
- Python 2.7 (www.python.org)
- pbcore (www.github.com/PacificBiosciences/pbcore)
- Blasr (www.github.com/PacificBiosciences/blasr)
- Mothur (www.mothur.org)
rDnaTools also includes the capability to generate high-quality consensus sequences from clusters of ribosomal DNA reads using algorithms included in the Pacific Biosciences SMRT Analysis suite.
- SMRTanalysis (www.pacbiodevnet.com)
rDnaTools contains two primary tools for analyzing rDNA sequence data
- rDnaPipeline
- rDnaResequencer
The rDnaPipeline takes as an input PacBio sequence data from ribosomal DNA amplicons, in either FOFN, BAS.H5, FASTA, or FASTQ formate, and runs a sequential series of analyses, similar to Mothur`s Batch Mode.
The rDnaResequencer tool generates consensus sequences from clusters of PacBio ribosomal DNA sequences. The Resequencer tool can be called either independently, or as part of the rDnaPipeline.
rDnaTools would not have been possible were it not for the hard work of the existing Microbial Ecology community, and their existing tools for analyzing ribosomal DNA sequence data. Since the core of the analyses wrapped by rDnaTools come from the Mothur suite, please cite their publication if you use rDnaTools in your work:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.