egads

Electronically Guided Digestion Selection - A ddRAD-seq enzyme selection aid

Installation

Install egads from this repository with the following command.

git clone --recursive https://github.com/IGBB/egads
make -C egads/src

Binary releases for Windows, macOS, and Linux are available on the Releases page and are released every six months to account for potential updates to the enzyme database.

Running

egads requires three arguments: 1) --rare: a comma-delimited list of rare cutting restriction enzymes, 2) --freq: a comma-delimited list of frequent cutting restriction enzymes, and 3) --genome: a fasta file, optionally compressed with gzip. The default output is an html report (see example.html) to stdout. The arguments --html, html report, and --bed, fragments in bed format, can be used to direct the output elsewhere.

./egads --rare <rare[,...]> --freq <freq[,...]> --genome <fasta[.gz]> > <output>

Restriction Enzymes

The restriction enzymes are downloaded from REBASE ( http://rebase.neb.com/rebase/rebase.html ) when compiling egads. A complete list of enzyme names can be found at http://rebase.neb.com/cgi-bin/acrolist; however, it may be more helpful to look through the various subsets available at http://rebase.neb.com/rebase/rebase.charts.html .

Testing

To recreate the report used in the "Innovations in ddRAD-seq" paper ( https://doi.org/10.1016/j.ab.2022.115001 ), download the G. longicalyx genome and run the following (will take a few minutes):

./egads --rare NsiI,HindII,PstI \
        --freq Sau3AI,BfaI,MspI,HinP1I \
        --genome longicalyx.fasta.gz \
        --html longicalyx.egads.html

In the example, I downloaded the genome in the same directory as the egads executable, and will output the report longicalyx.egads.html in that directory; however, any relative or absolute path should work.