ExtrAssembly

extrAssembly is a free, open‑source computational tool developed for the refinement and extraction of high‑quality genomic contigs from draft assemblies. Designed by a consortium of bioinformaticians from the University of Heidelberg and the National Center for Biotechnology Information, it first appeared as a preprint in the Bioinformatics open source repository in 2022 and was released under the MIT license later that year. The software accepts as input raw contig files in FASTA format, optional read mappings, and a set of optional scoring parameters, and it produces a curated set of contigs with improved continuity and accuracy. extrAssembly’s core algorithm combines iterative polishing steps with a graph‑based assessment of assembly metrics such as N50 and mis‑assembly frequency, allowing users to specify thresholds for merging or splitting contigs before final output. The package is written in Python 3 and depends on NumPy, Pandas, and Biopython; it can be run from the command line or imported as a library in other pipelines. Although primarily aimed at bacterial genome projects, extrAssembly has been employed in large eukaryotic assembly projects, including several metagenomic studies, where it has demonstrated an average increase in assembly completeness of 12 %. Documentation, including usage examples and a detailed API reference, is available on the project’s GitHub repository under the docs directory.