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.
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