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Marcela Uliano‐Silva, João Gabriel R. N. Ferreira, Ksenia Krasheninnikova, Mark Blaxter, Nova Mieszkowska, Neil Hall, Peter W. H. Holland, Richard Michael Durbin, Thomas A. Richards, Paul Julian Kersey and 17 more
BACKGROUND: PacBio high fidelity (HiFi) sequencing reads are both long (15-20 kb) and highly accurate (> Q20). Because of these properties, they have revolutionised genome assembly leading to more accurate and contiguous genomes. In eukaryotes the mitochondrial genome is sequenced alongside the nuclear genome often at very high coverage. A dedicated tool for mitochondrial genome assembly using HiFi reads is still missing. RESULTS: MitoHiFi was developed within the Darwin Tree of Life Project to assemble mitochondrial genomes from the HiFi reads generated for target species. The input for MitoHiFi is either the raw reads or the assembled contigs, and the tool outputs a mitochondrial genome sequence fasta file along with annotation of protein and RNA genes. Variants arising from heteroplasmy are assembled independently, and nuclear insertions of mitochondrial sequences are identified and not used in organellar genome assembly. MitoHiFi has been used to assemble 374 mitochondrial genomes (368 Metazoa and 6 Fungi species) for the Darwin Tree of Life Project, the Vertebrate Genomes Project and the Aquatic Symbiosis Genome Project. Inspection of 60 mitochondrial genomes assembled with MitoHiFi for species that already have reference sequences in public databases showed the widespread presence of previously unreported repeats. CONCLUSIONS: MitoHiFi is able to assemble mitochondrial genomes from a wide phylogenetic range of taxa from Pacbio HiFi data. MitoHiFi is written in python and is freely available on GitHub ( https://github.com/marcelauliano/MitoHiFi ). MitoHiFi is available with its dependencies as a Docker container on GitHub (ghcr.io/marcelauliano/mitohifi:master).
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Uliano‐Silva, M., Ferreira, J. G. R. N., Krasheninnikova, K., Blaxter, M., Mieszkowska, N., Hall, N., Holland, P. W. H., Durbin, R. M., Richards, T. A., Kersey, P. J., Hollingsworth, P. M., Wilson, W., Twyford, A. D., Gaya, E., Lawniczak, M., Lewis, O. T., Broad, G. R., Martin, F. J., Hart, M. L., … McCarthy, S. (2023). MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads. BMC Bioinformatics, 24(1), 288. https://doi.org/10.1186/s12859-023-05385-y
Uliano‐Silva, Marcela, et al. "MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads." BMC Bioinformatics, vol. 24, no. 1, 2023, pp. 288, https://doi.org/10.1186/s12859-023-05385-y.
Uliano‐Silva, Marcela, João Gabriel R. N. Ferreira, Ksenia Krasheninnikova, Mark Blaxter, Nova Mieszkowska, Neil Hall, Peter W. H. Holland, et al. "MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads." BMC Bioinformatics 24, no. 1 (2023): 288. https://doi.org/10.1186/s12859-023-05385-y.
Uliano‐Silva M., Ferreira J. G. R. N., Krasheninnikova K. [и др.] MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads // BMC Bioinformatics. — 2023. — Vol. 24, № 1. — P. 288. — URL: https://doi.org/10.1186/s12859-023-05385-y
@article{ulianosilva2023mitohifi,
title = {{MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads}},
author = {Marcela Uliano‐Silva and João Gabriel R. N. Ferreira and Ksenia Krasheninnikova and Mark Blaxter and Nova Mieszkowska and Neil Hall and Peter W. H. Holland and Richard Michael Durbin and Thomas A. Richards and Paul Julian Kersey and Peter M. Hollingsworth and Willie Wilson and Alex D. Twyford and Ester Gaya and Mara Lawniczak and Owen T. Lewis and Gavin R. Broad and Fergal J. Martin and Michelle L. Hart and Ian Barnes and Giulio Formenti and Linelle Ann L. Abueg and James Torrance and Eugene Wimberly Myers and Richard Michael Durbin and Mark Blaxter and Shane McCarthy},
journal = {BMC Bioinformatics},
year = {2023},
volume = {24},
number = {1},
pages = {288},
doi = {10.1186/s12859-023-05385-y},
url = {https://doi.org/10.1186/s12859-023-05385-y}
}TY - JOUR AU - Uliano‐Silva, Marcela AU - Ferreira, João Gabriel R. N. AU - Krasheninnikova, Ksenia AU - Blaxter, Mark AU - Mieszkowska, Nova AU - Hall, Neil AU - Holland, Peter W. H. AU - Durbin, Richard Michael AU - Richards, Thomas A. AU - Kersey, Paul Julian AU - Hollingsworth, Peter M. AU - Wilson, Willie AU - Twyford, Alex D. AU - Gaya, Ester AU - Lawniczak, Mara AU - Lewis, Owen T. AU - Broad, Gavin R. AU - Martin, Fergal J. AU - Hart, Michelle L. AU - Barnes, Ian AU - Formenti, Giulio AU - Abueg, Linelle Ann L. AU - Torrance, James AU - Myers, Eugene Wimberly AU - Durbin, Richard Michael AU - Blaxter, Mark AU - McCarthy, Shane TI - MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads JO - BMC Bioinformatics VL - 24 IS - 1 SP - 288 PY - 2023 DA - 2023/07/18 DO - 10.1186/s12859-023-05385-y UR - https://doi.org/10.1186/s12859-023-05385-y ER -
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