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