Please visit this Github site for the latest AlignGraph2 version.
AlignGraph2 is the second version of AlignGraph for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome.
If you use AlignGraph2, please cite the following paper:
Huang, S., He, X., Wang, G., & Bao, E. (2021). AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads. Briefings in Bioinformatics: epub.
Linux OS 64-bit
GCC >= 4.8.5
CMake >= 3.1.0
Python >= 3.6 with Biopython
git clone --recursive https://github.com/Godotcoffee/AlignGraph2.git
cd AlignGraph2 && python ./install.py
python ./AlignGraph2.py -r /path/to/read -c /path/to/contig -g /path/to/genome -o /path/to/output
-r, --read [fastq]
, long read file
-c, --contig [fasta]
, contig file
-g, --genome [fasta]
, similar genome file
-o, --output [dir]
, output directory
-m
, customized alignment algorithm mecat2ref+ (default: none)
-b [int]
, size of similar genome blocks for mecat2ref+ (default: 200)
--alpha [real]
, lower bound of k-mer scoring function for mecat2ref+ (default: 0.5)
--beta [real]
, upper bound of k-mer scoring function for mecat2ref+ (default: 2.0)
--delta [real]
, threshold for alignment scoring (default: 0.9)
-v [int]
, coverage to filter alignments (default: 2)
-k [int]
, size of k-mers in A-Bruijn graph (default: 14)
--epsilon [int]
, distance to join two vertices in A-Bruijn graph (default: 10)
-l [int]
, minimum path length for graph traversal (default: 50)
-a [int]
, size of long read blocks for consensus (default: 10,000)
-t [int]
, number of threads (default: 16)