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Common workflow language (CWL)-based software pipeline for de novo genome assembly from long- and short-read data

Autor

Pasi K. Korhonen

Robin B. Gasser

veröffentlicht in: GigaScience

Erscheinungsdatum: 2019-04-01

Sprache: Englisch

Hauptthema: genome assembly, Wiederholpräzision

Zitiert Artikel 71

Datum

Titel

Autor

2018-02-01

A Genome Resequencing-Based Genetic Map Reveals the Recombination Landscape of an Outbred Parasitic Nematode in the Presence of Polyploidy and Polyandry

Stephen R. Doyle, Roz Laing, John Gilleard, Alan Tracey
2018-02-15

Improved genomic resources and new bioinformatic workflow for the carcinogenic parasite Clonorchis sinensis: Biotechnological implications.

Daxi Wang, Pasi K. Korhonen, Robin B. Gasser, Neil D Young
2018-06-01

Practical Computational Reproducibility in the Life Sciences

John Chilton, Nicola Soranzo, James Taylor, Rolf Backofen, Anton Nekrutenko, Johannes Köster, Björn A Grüning, Jeremy Goecks, Marius van den Beek, Ryan K Dale
2018-07-01

Bioconda: sustainable and comprehensive software distribution for the life sciences

Christopher H Tomkins-Tinch, Johannes Köster, Renan Valieris, Jillian Rowe, Björn A Grüning, Andreas Sjödin, Ryan K Dale
2017-02-15

Detection and quantification of soil-transmitted helminths in environmental samples: A review of current state-of-the-art and future perspectives

Isaac Dennis Amoah
2017-03-06

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

Sergey Koren, John Schwartz, Derek M Bickhart, Joyce Lee, Heather J Huson, Alessandra Crisà, F. A. Ponce de León, John A Hammond, Steven G Schroeder, Maitreya Dunham, Adam Phillippy, Jay Shendure, Benjamin D Rosen, Jiajie Sun, Tad Sønstegård, Curt Van Tassell‬, Jana L Hutchison, Geoffrey C Waldbieser, Alex R Hastie
2017-03-15

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

Jason R. Miller, Sergey Koren, Adam Phillippy, Brian P Walenz, Nicholas H. Bergman
2017-04-01

Toil enables reproducible, open source, big biomedical data analyses

Gad Getz, David Haussler, Arjun Arkal Rao, Adam Novak, Anthony D Joseph, Benedict Paten, Kate R. Rosenbloom, Jim Kent
2017-05-11

Singularity: Scientific containers for mobility of compute

Vanessa V. Sochat
2017-06-05

Differential analysis of RNA-seq incorporating quantification uncertainty

Páll Melsted, Lior Pachter
2017-10-01

Single-Molecule Sequencing Reveals the Chromosome-Scale Genomic Architecture of the Nematode Model Organism Pristionchus pacificus.
2016-03-05

Making sense of genomes of parasitic worms: Tackling bioinformatic challenges

Pasi K. Korhonen, Neil D Young, Robin B. Gasser
2016-03-24

A review of bioinformatic pipeline frameworks

Jeremy Leipzig
2016-05-09

Human anthelminthic vaccines: Rationale and challenges

Peter Hotez, Sara Lustigman, Maria Elena Bottazzi, Ulrich Strych
2016-05-01

Coming of age: ten years of next-generation sequencing technologies

John McPherson
2016-06-26

Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11 kb), single molecule, real-time sequencing
2016-10-01

Global, regional, and national disability-adjusted life-years (DALYs) for 315 diseases and injuries and healthy life expectancy (HALE), 1990-2015: a systematic analysis for the Global Burden of Disease Study 2015

Benn Sartorius, Khurshid Alam, Sadaf G. Sepanlou, Alireza Mohammadi, Erkin Mirrachimow, Mohammad T. Hedayati, Maysaa El Sayed Zaki, Mostafa Qorbani, Samer Hamidi, Robyn M Lucas, Erika Ota, Olalekan A. Uthman, Amitava Banerjee, Ricky Leung, Chandrashekhar T. Sreeramareddy, Kalpana Balakrishnan, Gelin Xu, Andrew H Kemp, Seok Jun Yoon, Maheswar Satpathy, Samir Bhatt, Hamid Ahmadieh, Tissa Wijeratne, Gizachew Assefa Tessema, João V. Santos, Ferrán Catalá-López, Gholamreza Roshandel, Raimundas Lunevicius, Yuming Guo, David M. Pereira, Jung-Chen Chang, Alireza Esteghamati, Marcella Montico, Simon Hay, Farhad Pishgar, Amador Goodridge, Liliana G Ciobanu, Noore K Alam, Richard C. Franklin, Jose Martinez-Raga, Konstantinos Stroumpoulis, Francis A. Mhimbira, Matthew M Coates, Hassan Amini, Ilana Ackerman, Dan Kajungu, Bulat Idrissow, James Dean Wilkinson, Jonathan Carapetis
2016-11-10

Does antimalarial mass drug administration increase or decrease the risk of resistance?

Nicholas White
2016-10-17

Centrifuge: rapid and sensitive classification of metagenomic sequences.

Steven Salzberg, Daehwan Kim, Florian P Breitwieser
2016-01-01

RABIX: AN OPEN-SOURCE WORKFLOW EXECUTOR SUPPORTING RECOMPUTABILITY AND INTEROPERABILITY OF WORKFLOW DESCRIPTIONS.
2016-11-28

Database Resources of the National Center for Biotechnology Information.
2016-04-06

Modelling the health impact and cost-effectiveness of lymphatic filariasis eradication under varying levels of mass drug administration scale-up and geographic coverage

Christopher M Stone, Fabrizio Tediosi, Marcel Tanner
2015-02-04

Genetic blueprint of the zoonotic pathogen Toxocara canis

Pasi K. Korhonen, Neil D Young, Peter Nejsum, Qiye Li, Andreas Hofmann, Robin B. Gasser, Xiaodong Fang, Georg von Samson-Himmelstjerna, Aaron R Jex, Peter R. Boag, Xing-Quan Zhu, Paul W. Sternberg, Ross S Hall, Huimin Cai
2015-02-16

Improved data analysis for the MinION nanopore sequencer

Benedict Paten, Karen H Miga
2015-03-21

The laboratory domestication of Caenorhabditis elegans

Mark G. Sterken, Basten Snoek, Erik C Andersen
2015-06-09

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

Robert M. Waterhouse, Panagiotis Ioannidis
2015-06-01

Misassembly detection using paired-end sequence reads and optical mapping data

Simon J Puglisi
2015-10

Diverse Applications of Environmental DNA Methods in Parasitology

Grant D. Stentiford, David Bass
2015-10-07

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome
2015-10-01

PacBio Sequencing and Its Applications

Anthony Rhoads
2015-12-29

Circlator: automated circularization of genome assemblies using long sequencing reads

Martin Hunt, Thomas D. Otto, Nishadi De Silva, Jacqueline A Keane, Julian Parkhill
2014-04-01

Trimmomatic: a flexible trimmer for Illumina sequence data

Björn Usadel, Anthony M. Bolger

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