Complete-contigs

An assembler of unitigs, Y-to-V contigs and omnitigs.

1. Installation

In src directory, run

make

This places the executable complete-contigs in the directory bin.

If you want to install the program for removing non-maximal omnitigs, In src directory, run

make maximality

2. Usage

complete-contigs OPTIONS

Brief example:

complete-contigs -i <input .fa file>  -k 31 -g circular [-a 2] [-t 8]

Options:

-h, --help            show this help message and exit
--version             show program's version number and exit
-i STRING, --input=STRING
                    input file (.fasta/.fa/.fastq)
-k INT, --kmersize=INT
                    kmer size (default: 31)
-a INT, --abundance=INT
                    minimum abundance (default: 1)
-t INT, --threads=INT
                    number of threads, in [1..16] (default: 1)
-g STRING, --genome-type=STRING
                    genome type: linear|circular (default: circular)
-b, --build-only      build the de bruijn graph and then exit
-d, --printdot        print the graph in dot format
-x, --noomnitigs      do not compute omnitigs
-c, --nocontract      do not contract arcs. WARNING: option used only for
                    debugging; activating this option make the unitg
                    algorithm report less and shorter unitigs
-l, --nolength2opt    do not use the optimization with length-2 omnitigs.
                    WARNING: used for testing purposes.

3. Removing non-maximal omnitigs

The outputted unitigs and Y-to-V contigs are maximal, but omnitigs are not necessarily. To remove non-maximal omnitigs, run for example

bin/maximality chr10.k55.circular.omnitigs