PLAST - Pangenome Local Alignment Search Tool
PLAST is a freely available command line tool enabling the heuristic search for highest scoring local alignments between a nucleotide sequence query and a graphical pangenome consisting of thousands of individual genomes. Input pangenomes may be given either as an existing sequence graph or as sets of (multiple) FASTA or FASTQ files containing complete genomes, assembled contigs, or raw sequencing reads. Highest scoring local alignments between a query and all sequences of the pangenome are searched based on a seed-and-extend approach. Alignment outputs may be enriched with information about the individual genomes whose sequences are involved in an alignment. A search may be restricted to specific parts a the pangenome with respect to sequence presence in certain individual genomes or with respect to their abundance among individual genomes.
Neither development nor maintenance funded by de.NBI.