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MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads.
Uliano-Silva, Marcela; Ferreira, João Gabriel R N; Krasheninnikova, Ksenia; Formenti, Giulio; Abueg, Linelle; Torrance, James; Myers, Eugene W; Durbin, Richard; Blaxter, Mark; McCarthy, Shane A.
Afiliação
  • Uliano-Silva M; Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK. mu2@sanger.ac.uk.
  • Ferreira JGRN; Bio Bureau Biotecnologia, Rio de Janeiro, Brazil.
  • Krasheninnikova K; Instituto de Biofísica Carlos Chagas Filho, UniversidadeFederal Do Rio de Janeiro, Rio de Janeiro, Brazil.
  • Abueg L; The Rockefeller University, New York, NY, USA.
  • Torrance J; The Rockefeller University, New York, NY, USA.
  • Myers EW; Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK.
  • Durbin R; Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
  • Blaxter M; Okinawa Institute of Science and Technology, Okinawa, Japan.
  • McCarthy SA; Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK.
BMC Bioinformatics ; 24(1): 288, 2023 Jul 18.
Article em En | MEDLINE | ID: mdl-37464285
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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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Genoma Mitocondrial Idioma: En Ano de publicação: 2023 Tipo de documento: Article

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Genoma Mitocondrial Idioma: En Ano de publicação: 2023 Tipo de documento: Article