TRegGA: Targeted Reference-guided Genome Assembly for Comparative Rice Genomics

TRegGA is a fully automated workflow designed for locus-scale analysis of rice genomes, especially those sequenced in the 3k Rice Genomes Project (3kRGP). It is free open-source software, and utilizes a variety of third-party software for retrieving, processing, and annotating genome data. TRegGA offers a richer view of rice genome variation than SNP databases, as it uses genome assembly to capture the entire genomic context in a way that cannot be done with mapping against a reference.

Getting Started

See INSTALL.md for a detailed installation manual. Once TRegGA is configured and all software prerequisites are installed, complete the installation by executing bash setup.sh in your terminal. This will download and preprare reference genomes and other ancillary data required by the TRegGA workflow. The scripts check-prereqs.sh and check-data.sh have been provided to assist in troubleshooting software installation and data retrieval, respectively.

We do not yet have a small automated test to verify that TRegGA is working properly. In the mean time, see VIGNETTE.txt for some examples that can be used for testing.

Note: TRegGA is not designed to run on a latop. You'll want a machine with plenty of storage space and a fast Internet connection.

Troubleshooting

If you have trouble installing or running TRegGA, feel free to open a ticket in our issue tracker.

Synopsis

A typical TRegGA workflow involves the following.

• Illumina reads from a specific rice cultivar
• A reference genome (indica or japonica)
• A target locus of interest
• Assembly of the specified target in the given cultivar (de novo first, then reference-guided)

Data retrieval and workflow execution is implemented and documented in aptly named sub-directories.

• reads/: retrieval and storage of Illumina reads to be assembled; reads are retrieved for each cultivar as needed; see reads/README.md

• reference/: storage of reference genomes; contains subdirectories rice_indica and rice_japonica; data is retrieved and processed during the initial setup procedure

• targets/: storage of target sequences; typically, these targets would be derived from reference sequences by specifying a particular region (and transferring the annotation to the new coordinate system)

• assembly/denovo/: SOAPdenovo2 assemblies of reads to contigs and scaffolds, optionally gap-filled with GapFiller

• assembly/rfguided/: reference-guided assemblies of reads using the specified target as a template; this step involves AlignGraph, ABACAS, GapFiller, and RATT