MicroFinder

MicroFinder enables faster and more accurate assembly of bird DNA into chromosomallly resolved genome assemblies. Improved genome assemblies will help guide and improve conservation efforts by allowing researchers to study and better understand bird biology and evolution.

MicroFinder is a pipeline that aids the curation of bird genome assemblies by identifying putative microchromosome scaffolds and moving them to start of the genome assembly FASTA file. The resulting Microfinder-ordered assembly file can be used to make a Hi-C contact map for downstream manual curation.

The MicroFinder pipeline uses miniprot to map a set of conserved microchromosome-associated proteins to a draft assembly and then counts the resulting hits and orders the input assembly by the number hits. Optionally, a maximum scaffold length cutoff can be set – this causes scaffolds shorter than the cutoff to be sorted by MicroFinder protein hits and scaffolds longer than the cutoff to be sorted by length.

MicroFinder-enabled manual curation:

Details of the MicroFinder pipeline are in our paper:

MicroFinder: conserved gene-set mapping and assembly ordering for manual curation of bird dot microchromosomes. Gigascience 2026 Apr 3:giag036. DOI: 10.1093/gigascience/giag036.

Downloads

MicroFinder is available for download on GitHub

Further information

Learn and support

A tutorial on using MicroFinder to aid bird genome curation with example datasets can be found here: https://zenodo.org/records/13913870.