RADProc, an algorithm and software package that streamlines and accelerates de novo locus formation and catalog building by eliminating redundancies and using a highly efficient method for nucleotide distance calculation. RADProc can efficiently sweep through different sets of parameters for de novo locus formation and catalog building. Although RADProc is an alternative method for de novo locus formation and catalog building from RADseq data, the output files generated by RADProc are completely compatible with the Stacks pipeline.

The RADProc software is implemented in C++ and parallelized using the OpenMP libraries. RADProc can be complied in GNU-based Linux systems or BSD-based OS X systems. It is released under GNU GPL license.

Download the source files from https://github.com/beiko-lab/RADProc

In the Terminal:

• Unzip the downloaded zip file.

• Traverse to the folder "Install".

$autoreconf --install
$sh ./configure
$ make
root access or sudo 
$ make install

RADProc will be installed in the path “ /usr/local/bin “

RADProc -t infile_type -f file_path [-o path][-a psweep][-M max_dist] [-m min_cov][-n max_cat_dist][-p num_threads] [-x max_stacks][-S min_sam][-D min_depth][-h]

t: Input file Type. Supported types: fasta, fastq, gzfasta, or gzfastq.

f: Input file path.

o: Output path to write results.

a: Enable parameter sweep mode.

M: Maximum distance (in nucleotides) allowed between stacks to form network.

m: Minimum coverage depth.

n: Maximum distance (in nucleotides) allowed between catalog loci to merge

p: Enable parallel execution with num_threads threads.

x: Maximum number stacks per locus.

S: Minimum sample percentage.

D: Minimum average coverage depth.

h: Display this help messsage.

Input filenmes should be 3 character population code followed by the sample ID. Example: AAA1.fq, AAA2.fq, BBB1.fq.