Pacbio Graph Overlapper
This elementary version consists of 4 programs:
You can install this by following command:
make
You need to install biopython, networkx and networKit before using this tool.
1. create_ABruijn.py : This creates K-mer graph from reads and stores it in gml file.
usage: create_ABruijn.py [-h] [-r PACBIO_READS] [-k KMER_SIZE] [-c KMER_COUNT]
[-f FILTER] [-o OUTPUT_FILE]
optional arguments:
-h, --help show this help message and exit
-r PACBIO_READS, --pacbio_reads PACBIO_READS
input pacbio long reads
-k KMER_SIZE, --kmer_size KMER_SIZE
kmer_size
-c KMER_COUNT, --kmer_count KMER_COUNT
file containing list of kmers
-f FILTER, --filter FILTER
kmer cutoff filter
-o OUTPUT_FILE, --output_file OUTPUT_FILE
graph to be output
2. create_links.cpp : This create links between k-mers in K-mer graph.
usage: ./create_links --reads=string --edgefile=string --nodefile=string --kmercount=string --kmersize=int [options] ...
options:
-r, --reads pacbio reads (string)
-e, --edgefile edgefile of kmers (string)
-n, --nodefile nodefile (string)
-c, --kmercount kmercount (string)
-k, --kmersize kmersize (int)
-?, --help print this message
3. Louvain_label.cpp : Generates labeling of nodes in K-mer graphs using louvain clustering
usage: ./louvain --dbg=string --read_to_node=string --label_file=string [options] ...
options:
-g, --dbg de bruijn graph of reads (string)
-r, --read_to_node read to node mapping (string)
-o, --label_file outputfle (string)
-?, --help print this message
4. avg_neighborhood.cpp: Predicts overlap using neighborhood information and outputs like BLASR m4 format.
usage: ./avg_neighrhood --reads=string --edgefile=string --nodefile=string --kmersize=int --output=string [options] ...
options:
-r, --reads pacbio reads (string)
-e, --edgefile edgefile of kmers (string)
-n, --nodefile nodemapping (string)
-k, --kmersize kmersize (int)
-o, --output output (string)
-?, --help print this message
5. kmer_count.py: Generates kmer counts from reads.
usage: kmer_count.py [-h] [-r PACBIO_READS] [-k KMER_SIZE] [-o OUTPUT_FILE]
optional arguments:
-h, --help show this help message and exit
-r PACBIO_READS, --pacbio_reads PACBIO_READS
input pacbio long reads
-k KMER_SIZE, --kmer_size KMER_SIZE
kmer_size
-o OUTPUT_FILE, --output_file OUTPUT_FILE
output file