PGA is not an independent assembly software, it relies on the output of hifiasm and technologies that can anchor contigs to chromosomes,such as genetic maps, HIC, or alignment with genome sequences of related species to achieve a gapless genome.
python3
mummer
networkx
conda install -c bioconda mummer
conda install -c conda-forge networkx
git clone https://github.com/likui345/PGA.git
python setup.py install
usage: rbsa.py --type nucmer --ref REF --scf SCF or rbsa.py --type mcscan --A_bed A_BED --B_bed B_BED --anchor ANCHOR --scf SCF
optional arguments: -h, --help show this help message and exit --type {nucmer,mcscan} nucmer or mcscan anchor --ref REF This is reference genome sequences which has anchored to the chromosomal level --scf SCF This is the scaffold sequences --A_bed A_BED species_a bed file --B_bed B_BED species_b bed file --anchor ANCHOR anchor.simple files of species_a and species_b
usage: filter.py --paf_fn PAF --bestn NUM --output OUTPUT
optional arguments: -h, --help show this help message and exit --paf_fn PAF_FN Input. reads alignment file --bestn BESTN output at least best n overlaps on 5' or 3' ends if possible. --output OUTPUT Output filename
usage: chr_paths.py --agp AGP --gfa GFA
optional arguments: -h, --help show this help message and exit --agp AGP agp file form contig anchoring --gfa GFA gfa from hifiasm
usage: ovlp2graph.py [-h] --overlap-file OVERLAP_FILE
optional arguments: -h, --help show this help message and exit --overlap-file OVERLAP_FILE a file that contains the overlap information. (default: None)
Outputs: - sg_edges_list - chimer_nodes
usage: graph2chr.py [-h] --reads-fasta-fn READS_FASTA_FN --paf-fn PAF_FN --sg-edges-list-fn SG_EDGES_LIST_FN --ctg-paths-fn CTG_PATHS_FN
optional arguments: -h, --help show this help message and exit --reads-fasta-fn READS_FASTA_FN Input. reads file generated by hifiasm. (default: None) --paf-fn PAF_FN Input. reads alignment file generated by hifiasm. (default: None) --sg-edges-list-fn SG_EDGES_LIST_FN Input. File containing string graph edges, produced by ovlp2graph.py. (default: None) --ctg-paths-fn CTG_PATHS_FN Input. File containing contig paths. (default: None)