Polypolish: Short-read polishing of long-read bacterial genome assemblies

Autor: Ryan Wick, Kathryn Holt

Publikováno v: PLoS Computational Biology, Vol 18, Iss 1, p e1009802 (2022)
PLoS Computational Biology

Long-read-only bacterial genome assemblies usually contain residual errors, most commonly homopolymer-length errors. Short-read polishing tools can use short reads to fix these errors, but most rely on short-read alignment which is unreliable in repe

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a391a69e05764db835e0c757a49ced4a

Sequencing DNA with nanopores: Troubles and biases

Autor: Clara Delahaye, Jacques Nicolas

Publikováno v: PLoS ONE
PLoS ONE, 2021, pp.1-29. ⟨10.1371/journal.pone.0257521⟩
PLoS ONE, Public Library of Science, 2021, pp.1-29. ⟨10.1371/journal.pone.0257521⟩
PLoS ONE, Vol 16, Iss 10, p e0257521 (2021)

International audience; Oxford Nanopore Technologies' (ONT) long read sequencers offer access to longer DNA fragments than previous sequencer generations, at the cost of a higher error rate. While many papers have studied read correction methods, few

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid_dedup__::1325d627cafd5537be7fbe871aa61be0
https://hal.inria.fr/hal-03362956

The evolutionary history of topological variations in the CPA/AT transporters

Autor: Govindarajan Sudha, Claudio Bassot, John Lamb, Nanjiang Shu, Yan Huang, Arne Elofsson

Publikováno v: PLoS Computational Biology
PLoS Computational Biology, Vol 17, Iss 8, p e1009278 (2021)

CPA/AT transporters are made up of scaffold and a core domain. The core domain contains two non-canonical helices (broken or reentrant) that mediate the transport of ions, amino acids or other charged compounds. During evolution, these transporters h

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid_dedup__::225052d01e1bc308a484d7a46d8a29b3
http://europepmc.org/articles/PMC8396727

Performance and scaling behavior of bioinformatic applications in virtualization environments to create awareness for the efficient use of compute resources

Autor: Maximilian, Hanussek, Felix, Bartusch, Jens, Krüger

Publikováno v: PLoS Computational Biology, Vol 17, Iss 7, p e1009244 (2021)
PLoS Computational Biology

The large amount of biological data available in the current times, makes it necessary to use tools and applications based on sophisticated and efficient algorithms, developed in the area of bioinformatics. Further, access to high performance computi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid_dedup__::b0a23d98fa33942975ae26b0ad588e30
https://doaj.org/article/7a947ed7b5e046708e7eb5329b011793

Exogene: A performant workflow for detecting viral integrations from paired-end next-generation sequencing data

Autor: Daniel R. O'Brien, Mrunal Dehankar, Jean Pierre A. Kocher, Ravishankar K. Iyer, Zachary D. Stephens, Lewis R. Roberts

Publikováno v: PLoS ONE, Vol 16, Iss 9, p e0250915 (2021)
PLoS ONE

The integration of viruses into the human genome is known to be associated with tumorigenesis in many cancers, but the accurate detection of integration breakpoints from short read sequencing data is made difficult by human-viral homologies, viral ge

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6c2654667f70bf3a65c55d3e641f5bb3
https://doi.org/10.1101/2021.04.19.440427