Fix single target counts being incorrect (#212)

fix removal of edges paths
add new edges type: directional that encodes both single-sample >10X coverage and recovery samples
add new edges type: singleton that encodes >10X coverage targets not found in any other sample
increase chunk size so it finishes faster
add test for asymmetric directional edges
fix flakey test

Bin Chicken

Bin Chicken - recovery of low abundance and taxonomically targeted metagenome assembled genomes (MAGs) through strategic coassembly.

Documentation can be found at https://AroneyS.github.io/binchicken/

Logo by Georgina H. Joyce | www.georginajoyce.com

Not to be confused with https://gitlab.com/andreassh/binchicken

Citations

Aroney, S.T.N., Newell, R.J.P., Tyson, G.W. and Woodcroft B.J. Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes. Nat Methods (2025). https://doi.org/10.1038/s41592-025-02901-1.

Bin Chicken is built on the SingleM tool, which is described in the following publication:

Woodcroft B.J., Aroney, S.T.N., Zhao, R., Cunningham, M., Mitchell, J.A.M., Nurdiansyah, R., Blackall, L. & Tyson, G.W. Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper. Nat Biotechnol (2025). https://doi.org/10.1038/s41587-025-02738-1.

If you use Aviary (through --run-aviary), please see the Aviary documentation for how to cite Aviary and its underlying dependencies.