doepipeline: a systematic approach to optimizing multi-level and multi-step data processing workflows

Abstract Background Selecting the proper parameter settings for bioinformatic software tools is challenging. Not only will each parameter have an individual effect on the outcome, but there are also potential interaction effects between parameters. Both of these effects may be difficult to predict....

وصف كامل

التفاصيل البيبلوغرافية
الحاوية / القاعدة:	BMC Bioinformatics
المؤلفون الرئيسيون:	Daniel Svensson, Rickard Sjögren, David Sundell, Andreas Sjödin, Johan Trygg
التنسيق:	مقال
اللغة:	الإنجليزية
منشور في:	BMC 2019-10-01
الموضوعات:	Design of Experiments Optimization Sequencing Nanopore MinION Assembly
الوصول للمادة أونلاين:	http://link.springer.com/article/10.1186/s12859-019-3091-z

مواد مشابهة

First transcriptome sequencing, assembly, and annotation dataset for the freshwater angelfish, pterophyllum scalare
حسب: Indeever Madireddy
منشور في: (2024-06-01)

Real-Time On-Site Diagnosis of Quarantine Pathogens in Plant Tissues by Nanopore-Based Sequencing
حسب: Luca Marcolungo, وآخرون
منشور في: (2022-02-01)

Draft Assembly of Phytophthora capsici from Long-Read Sequencing Uncovers Complexity
حسب: Chenming Cui, وآخرون
منشور في: (2019-12-01)

MinION nanopore sequencing of an influenza genome
حسب: Jing eWang, وآخرون
منشور في: (2015-08-01)

High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies
حسب: Jared T. Broddrick, وآخرون
منشور في: (2020-11-01)

Nanopore sequencing and full genome de novo assembly of human cytomegalovirus TB40/E reveals clonal diversity and structural variations
حسب: Timokratis Karamitros, وآخرون
منشور في: (2018-08-01)

FINISHING THE JOB - UTILITY OF LONG-READ SEQUENCING USING THE MINION FOR BACTERIAL GENOMICS
حسب: Amada El-Sabeh
منشور في: (2021-08-01)

Custom barcoded primers for influenza A nanopore sequencing: enhanced performance with reduced preparation time
حسب: Iryna V. Goraichuk, وآخرون
منشور في: (2025-04-01)

Improved influenza A whole-genome sequencing protocol
حسب: Iryna V. Goraichuk, وآخرون
منشور في: (2024-11-01)

Nanopore sequencing reveals genomic map of CTX-M-type extended-spectrum β-lactamases carried by Escherichia coli strains isolated from blue mussels (Mytilus edulis) in Norway
حسب: Didrik H. Grevskott, وآخرون
منشور في: (2020-05-01)

Comprehensive Pathogen Identification, Antibiotic Resistance, and Virulence Genes Prediction Directly From Simulated Blood Samples and Positive Blood Cultures by Nanopore Metagenomic Sequencing
حسب: Menglan Zhou, وآخرون
منشور في: (2021-03-01)

Identification of Genomic Variants of SARS-CoV-2 Using Nanopore Sequencing
حسب: Ionut Dragos Capraru, وآخرون
منشور في: (2022-12-01)

Rapid diagnosis of Mycobacterium marinum infection using targeted nanopore sequencing: a case report
حسب: Yan-Ying Huang, وآخرون
منشور في: (2023-10-01)

Case Report: BMPR2-Targeted MinION Sequencing as a Tool for Genetic Analysis in Patients With Pulmonary Arterial Hypertension
حسب: Tomoya Takashima, وآخرون
منشور في: (2021-09-01)

Rapid genotyping of Toxoplasma gondii isolates via Nanopore-based multi-locus sequencing
حسب: Zisis Koutsogiannis, وآخرون
منشور في: (2024-06-01)

Portable Rabies Virus Sequencing in Canine Rabies Endemic Countries Using the Oxford Nanopore MinION
حسب: Crystal M. Gigante, وآخرون
منشور في: (2020-11-01)

Development and validation of a long-read metabarcoding platform for the detection of filarial worm pathogens of animals and humans
حسب: Lucas G. Huggins, وآخرون
منشور في: (2024-01-01)

Balancing read length and sequencing depth: Optimizing Nanopore long‐read sequencing for monocots with an emphasis on the Liliales
حسب: Gisel Y. De La Cerda, وآخرون
منشور في: (2023-05-01)

An innovative diagnostic technology for the codon mutation C580Y in kelch13 of Plasmodium falciparum with MinION nanopore sequencer
حسب: Kazuo Imai, وآخرون
منشور في: (2018-05-01)

Rapid virulence prediction and identification of Newcastle disease virus genotypes using third-generation sequencing
حسب: Salman L. Butt, وآخرون
منشور في: (2018-11-01)

Microbiome dataset analysis from a shrimp pond in Ninh Thuan, Vietnam using shotgun metagenomics
حسب: Lan-Anh Le, وآخرون
منشور في: (2020-08-01)

Rapid multiplex MinION nanopore sequencing workflow for Influenza A viruses
حسب: Jacqueline King, وآخرون
منشور في: (2020-09-01)

Cattle connection: molecular epidemiology of BVDV outbreaks via rapid nanopore whole-genome sequencing of clinical samples
حسب: Jacqueline King, وآخرون
منشور في: (2021-07-01)

Mycobiome of low maintenance iconic landscape plant boxwood under repeated treatments of contact and systemic fungicides
حسب: Xiaoping Li, وآخرون
منشور في: (2025-08-01)

The 28S rRNA RT-qPCR assay for host depletion evaluation to enhance avian virus detection in Illumina and Nanopore sequencing
حسب: Iryna V. Goraichuk, وآخرون
منشور في: (2024-01-01)

Rapid diagnosis of fatal Nocardia kroppenstedtii bacteremic pneumonia and empyema thoracis by next-generation sequencing: a case report
حسب: Fanfan Xing, وآخرون
منشور في: (2023-07-01)

Universal amplification and sequencing of foot-and-mouth disease virus complete genomes using nanopore technology
حسب: Andrew E. Shaw, وآخرون
منشور في: (2025-08-01)

DNA Barcoding for Species Identification of Moss-Dwelling Invertebrates: Performance of Nanopore Sequencing and Coverage in Reference Database
حسب: Stephan Koblmüller, وآخرون
منشور في: (2024-03-01)

Molecular Characterization of Newcastle Disease Viruses Isolated from Chickens in Tanzania and Ghana
حسب: Ana P. da Silva, وآخرون
منشور في: (2020-08-01)

Rapid detection of high consequence and emerging viral pathogens in pigs
حسب: Alison C. Neujahr, وآخرون
منشور في: (2024-02-01)

Assessing the utility of the Oxford Nanopore MinION for snake venom gland cDNA sequencing
حسب: Adam D. Hargreaves, وآخرون
منشور في: (2015-11-01)

Draft Genome Resource for Macrophomina phaseolina Associated With Charcoal Rot in Sorghum
حسب: Neeraj Purushotham, وآخرون
منشور في: (2020-05-01)

The geographical and seasonal effects on the composition of marine microplastic and its microbial communities: The case study of Israel and Portugal
حسب: Katherine S. Marsay, وآخرون
منشور في: (2023-02-01)

Whole-Genome Sequencing of Six Neglected Arboviruses Circulating in Africa Using Sequence-Independent Single Primer Amplification (SISPA) and MinION Nanopore Technologies
حسب: Ansgar Schulz, وآخرون
منشور في: (2022-12-01)

Towards Improved Nepovirus Detection and Identification in Xiphinema Nematodes
حسب: Ellen A. Everaert, وآخرون
منشور في: (2024-12-01)

Transmission of Similar Mcr-1 Carrying Plasmids among Different <i>Escherichia coli</i> Lineages Isolated from Livestock and the Farmer
حسب: Joaquim Viñes, وآخرون
منشور في: (2021-03-01)

CRISPR/Cas9 gene targeting plus nanopore DNA sequencing with the plasmid pBR322 in the classroom
حسب: Röbbe Wünschiers, وآخرون
منشور في: (2024-08-01)

Nanopore Sequencing Is a Credible Alternative to Recover Complete Genomes of Geminiviruses
حسب: Selim Ben Chehida, وآخرون
منشور في: (2021-04-01)

A new method for long-read sequencing of animal mitochondrial genomes: application to the identification of equine mitochondrial DNA variants
حسب: Sophie Dhorne-Pollet, وآخرون
منشور في: (2020-11-01)

Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing
حسب: Amrita Srivathsan, وآخرون
منشور في: (2019-11-01)