NanoPack2: population-scale evaluation of long-read sequencing data
Abstract Summary Increases in the cohort size in long-read sequencing projects necessitate more efficient software for quality assessment and processing of sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. Here, we describe novel tools for summarizing experiments, filtering...
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| Veröffentlicht in: | Bioinformatics (Oxford, England) Jg. 39; H. 5 |
|---|---|
| Hauptverfasser: | , |
| Format: | Journal Article |
| Sprache: | Englisch |
| Veröffentlicht: |
England
Oxford University Press
04.05.2023
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| ISSN: | 1367-4811, 1367-4803, 1367-4811 |
| Online-Zugang: | Volltext |
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| Abstract | Abstract
Summary
Increases in the cohort size in long-read sequencing projects necessitate more efficient software for quality assessment and processing of sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. Here, we describe novel tools for summarizing experiments, filtering datasets, visualizing phased alignments results, and updates to the NanoPack software suite.
Availability and implementation
The cramino, chopper, kyber, and phasius tools are written in Rust and available as executable binaries without requiring installation or managing dependencies. Binaries build on musl are available for broad compatibility. NanoPlot and NanoComp are written in Python3. Links to the separate tools and their documentation can be found at https://github.com/wdecoster/nanopack. All tools are compatible with Linux, Mac OS, and the MS Windows Subsystem for Linux and are released under the MIT license. The repositories include test data, and the tools are continuously tested using GitHub Actions and can be installed with the conda dependency manager. |
|---|---|
| AbstractList | Abstract
Summary
Increases in the cohort size in long-read sequencing projects necessitate more efficient software for quality assessment and processing of sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. Here, we describe novel tools for summarizing experiments, filtering datasets, visualizing phased alignments results, and updates to the NanoPack software suite.
Availability and implementation
The cramino, chopper, kyber, and phasius tools are written in Rust and available as executable binaries without requiring installation or managing dependencies. Binaries build on musl are available for broad compatibility. NanoPlot and NanoComp are written in Python3. Links to the separate tools and their documentation can be found at https://github.com/wdecoster/nanopack. All tools are compatible with Linux, Mac OS, and the MS Windows Subsystem for Linux and are released under the MIT license. The repositories include test data, and the tools are continuously tested using GitHub Actions and can be installed with the conda dependency manager. Increases in the cohort size in long-read sequencing projects necessitate more efficient software for quality assessment and processing of sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. Here, we describe novel tools for summarizing experiments, filtering datasets, visualizing phased alignments results, and updates to the NanoPack software suite.SUMMARYIncreases in the cohort size in long-read sequencing projects necessitate more efficient software for quality assessment and processing of sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. Here, we describe novel tools for summarizing experiments, filtering datasets, visualizing phased alignments results, and updates to the NanoPack software suite.The cramino, chopper, kyber, and phasius tools are written in Rust and available as executable binaries without requiring installation or managing dependencies. Binaries build on musl are available for broad compatibility. NanoPlot and NanoComp are written in Python3. Links to the separate tools and their documentation can be found at https://github.com/wdecoster/nanopack. All tools are compatible with Linux, Mac OS, and the MS Windows Subsystem for Linux and are released under the MIT license. The repositories include test data, and the tools are continuously tested using GitHub Actions and can be installed with the conda dependency manager.AVAILABILITY AND IMPLEMENTATIONThe cramino, chopper, kyber, and phasius tools are written in Rust and available as executable binaries without requiring installation or managing dependencies. Binaries build on musl are available for broad compatibility. NanoPlot and NanoComp are written in Python3. Links to the separate tools and their documentation can be found at https://github.com/wdecoster/nanopack. All tools are compatible with Linux, Mac OS, and the MS Windows Subsystem for Linux and are released under the MIT license. The repositories include test data, and the tools are continuously tested using GitHub Actions and can be installed with the conda dependency manager. Increases in the cohort size in long-read sequencing projects necessitate more efficient software for quality assessment and processing of sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. Here, we describe novel tools for summarizing experiments, filtering datasets, visualizing phased alignments results, and updates to the NanoPack software suite. The cramino, chopper, kyber, and phasius tools are written in Rust and available as executable binaries without requiring installation or managing dependencies. Binaries build on musl are available for broad compatibility. NanoPlot and NanoComp are written in Python3. Links to the separate tools and their documentation can be found at https://github.com/wdecoster/nanopack. All tools are compatible with Linux, Mac OS, and the MS Windows Subsystem for Linux and are released under the MIT license. The repositories include test data, and the tools are continuously tested using GitHub Actions and can be installed with the conda dependency manager. |
| Author | De Coster, Wouter Rademakers, Rosa |
| Author_xml | – sequence: 1 givenname: Wouter orcidid: 0000-0002-5248-8197 surname: De Coster fullname: De Coster, Wouter email: wouter.decoster@uantwerpen.vib.be – sequence: 2 givenname: Rosa orcidid: 0000-0002-4049-0863 surname: Rademakers fullname: Rademakers, Rosa |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/37171891$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1093/bioinformatics/bty149 10.1093/bioinformatics/btu590 10.1038/s41467-019-12493-y 10.1093/bioinformatics/bty191 10.1126/science.1072047 10.1093/bioinformatics/bty654 10.1038/s41588-021-00865-4 10.1038/s41576-021-00367-3 10.1093/bioinformatics/btv573 10.1093/gigascience/giab007 |
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| License | This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. https://creativecommons.org/licenses/by/4.0 The Author(s) 2023. Published by Oxford University Press. |
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| References | Beyter (2023051907505191200_btad311-B2) 2021; 53 Martin (2023051907505191200_btad311-B11) 2016 Leger (2023051907505191200_btad311-B9) 2020 Lanfear (2023051907505191200_btad311-B8) 2019; 35 De Coster (2023051907505191200_btad311-B5) 2021; 22 Li (2023051907505191200_btad311-B10) 2018; 34 Edge (2023051907505191200_btad311-B6) 2019; 10 Bailey (2023051907505191200_btad311-B1) 2002; 297 Köster (2023051907505191200_btad311-B7) 2016; 32 Watson (2023051907505191200_btad311-B13) 2015; 31 Bonfield (2023051907505191200_btad311-B3) 2021; 10 De Coster (2023051907505191200_btad311-B4) 2018; 34 Pereira (2023051907505191200_btad311-B12) 2017 |
| References_xml | – volume: 34 start-page: 2666 year: 2018 ident: 2023051907505191200_btad311-B4 article-title: NanoPack: visualizing and processing long-read sequencing data publication-title: Bioinformatics doi: 10.1093/bioinformatics/bty149 – volume: 31 start-page: 114 year: 2015 ident: 2023051907505191200_btad311-B13 article-title: poRe: an R package for the visualization and analysis of nanopore sequencing data publication-title: Bioinformatics doi: 10.1093/bioinformatics/btu590 – volume: 10 start-page: 4660 year: 2019 ident: 2023051907505191200_btad311-B6 article-title: Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing publication-title: Nat Commun doi: 10.1038/s41467-019-12493-y – volume: 34 start-page: 3094 year: 2018 ident: 2023051907505191200_btad311-B10 article-title: Minimap2: pairwise alignment for nucleotide sequences publication-title: Bioinformatics doi: 10.1093/bioinformatics/bty191 – volume: 297 start-page: 1003 year: 2002 ident: 2023051907505191200_btad311-B1 article-title: Recent segmental duplications in the human genome publication-title: Science doi: 10.1126/science.1072047 – volume: 35 start-page: 523 year: 2019 ident: 2023051907505191200_btad311-B8 article-title: MinIONQC: fast and simple quality control for MinION sequencing data publication-title: Bioinformatics doi: 10.1093/bioinformatics/bty654 – year: 2020 ident: 2023051907505191200_btad311-B9 – start-page: 256 year: 2017 ident: 2023051907505191200_btad311-B12 – year: 2016 ident: 2023051907505191200_btad311-B11 – volume: 53 start-page: 779 year: 2021 ident: 2023051907505191200_btad311-B2 article-title: Long-read sequencing of 3,622 icelanders provides insight into the role of structural variants in human diseases and other traits publication-title: Nat Genet doi: 10.1038/s41588-021-00865-4 – volume: 22 start-page: 572 year: 2021 ident: 2023051907505191200_btad311-B5 article-title: Towards population-scale long-read sequencing publication-title: Nat Rev Genet doi: 10.1038/s41576-021-00367-3 – volume: 32 start-page: 444 year: 2016 ident: 2023051907505191200_btad311-B7 article-title: Rust-Bio: a fast and safe bioinformatics library publication-title: Bioinformatics doi: 10.1093/bioinformatics/btv573 – volume: 10 start-page: 1 year: 2021 ident: 2023051907505191200_btad311-B3 article-title: HTSlib: C library for reading/writing high-throughput sequencing data publication-title: Gigascience doi: 10.1093/gigascience/giab007 |
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Increases in the cohort size in long-read sequencing projects necessitate more efficient software for quality assessment and processing of... Increases in the cohort size in long-read sequencing projects necessitate more efficient software for quality assessment and processing of sequencing data from... |
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| Title | NanoPack2: population-scale evaluation of long-read sequencing data |
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