asmapper

Asmapper is a name used by several software projects rather than a single, universally recognized tool. In practice, tools described as asmapper-type programs are designed to map assembled sequences or other data items to a reference structure, such as a genome, transcriptome, or coordinate system. Because the exact features vary by implementation, the following describes common characteristics found in many asmapper-style utilities.

In bioinformatics contexts, asmapper-style tools typically accept inputs such as de novo assembled contigs in FASTA format and a reference sequence set in FASTA or a precomputed reference genome. They produce alignment results that associate each contig with a reference coordinate or region and report metrics like alignment score, percent identity, and coverage. Methods may include seed-and-extend, hash-based matching, or minimizer-based strategies, with options to handle repetitive regions, chimeric contigs, and ambiguous mappings. Output formats often include coordinate-based reports and alignment files (for example, SAM/BAM-like outputs) to support downstream analyses.

Common applications include guiding genome finishing and scaffolding, transferring annotations from reference to assembly, and evaluating assembly quality through mapping statistics. Some implementations emphasize speed and scalability for large genomes, while others focus on accuracy in challenging regions.

Asmapper is not a single canonical project; rather, it describes a class of mapping tools with varying features and interfaces developed by different groups. In non-bio contexts, the term may also appear in data visualization or geospatial mapping as a generic “mapper” component for translating data to coordinates or views.

See also: genome assembly, sequence alignment, contig mapping, scaffolding, annotation transfer.