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/huangs001/AlignGraph2.git
cd AlignGraph2 && python ./install.pypython ./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)
To generate longer contigs, it is not avoidable that AlignGraph2 introduces additional misassemblies. Forturnately, it introduces much fewer misassemblies per mbp than the upstream de novo assembly algorithms.