Search Results - Bio-informatics pipeline/workflows

SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines by Lampa, Samuel, Dahlö, Martin, Alvarsson, Jonathan, Spjuth, Ola

“… SciPipe is a workflow programming library implemented in the programming language Go, for managing complex and dynamic pipelines in bioinformatics, cheminformatics, and other fields…”
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biogitflow: development workflow protocols for bioinformatics pipelines with git and GitLab [version 3; peer review: 2 approved] by Kamoun, Choumouss, Roméjon, Julien, de Soyres, Henri, Gallois, Apolline, Girard, Elodie, Hupé, Philippe

“…The use of a bioinformatics pipeline as a tool to support diagnostic and theranostic decisions in the healthcare process requires the definition of detailed development workflow guidelines…”
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AnVILWorkflow: A runnable workflow package for Cloud-implemented bioinformatics analysis pipelines [version 1; peer review: awaiting peer review] by Oh, Sehyun, Gravel-Pucillo, Kai, Ramos, Marcel, Schatz, Michael C., Davis, Sean, Carey, Vincent, Morgan, Martin, Waldron, Levi

“… However, utilizing the full capabilities of AnVIL can be challenging for researchers without extensive bioinformatics expertise, especially for executing complex workflows…”
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Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers by Wratten, Laura, Wilm, Andreas, Göke, Jonathan

“… commonly used approaches for bioinformatics workflows, and provide…”
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biogitflow: development workflow protocols for bioinformatics pipelines with git and GitLab [version 2; peer review: 1 approved, 1 approved with reservations] by Kamoun, Choumouss, Roméjon, Julien, de Soyres, Henri, Gallois, Apolline, Girard, Elodie, Hupé, Philippe

“…The use of a bioinformatics pipeline as a tool to support diagnostic and theranostic decisions in the healthcare process requires the definition of detailed development workflow guidelines…”
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biogitflow: development workflow protocols for bioinformatics pipelines with git and GitLab [version 1; peer review: 1 approved with reservations] by Kamoun, Choumouss, Roméjon, Julien, de Soyres, Henri, Gallois, Apolline, Girard, Elodie, Hupé, Philippe

“…The use of a bioinformatics pipeline as a tool to support diagnostic and theranostic decisions in the healthcare process requires the definition of detailed development workflow guidelines…”
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Building Infrastructure and Workflows for Clinical Bioinformatics Pipelines by Kadri, Sabah

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Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform by Li, Po-E, Lo, Chien-Chi, Anderson, Joseph J., Davenport, Karen W., Bishop-Lilly, Kimberly A., Xu, Yan, Ahmed, Sanaa, Feng, Shihai, Mokashi, Vishwesh P., Chain, Patrick S.G.

“… To address these issues, we have developed an intuitive web-based environment with a wide assortment of integrated and cutting-edge bioinformatics tools in pre-configured workflows…”
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Developing and reusing bioinformatics data analysis pipelines using scientific workflow systems by Djaffardjy, Marine, Marchment, George, Sebe, Clémence, Blanchet, Raphaël, Belhajjame, Khalid, Gaignard, Alban, Lemoine, Frédéric, Cohen-Boulakia, Sarah

“…Data analysis pipelines are now established as an effective means for specifying and executing bioinformatics data analysis and experiments…”
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Towards reproducible metabarcoding data: Lessons from an international cross‐laboratory experiment by Zaiko, Anastasija, Greenfield, Paul, Abbott, Cathryn, Ammon, Ulla, Bilewitch, Jaret, Bunce, Michael, Cristescu, Melania E., Chariton, Anthony, Dowle, Eddy, Geller, Jonathan, Ardura Gutierrez, Alba, Hajibabaei, Mehrdad, Haggard, Emmet, Inglis, Graeme J., Lavery, Shane D., Samuiloviene, Aurelija, Simpson, Tiffany, Stat, Michael, Stephenson, Sarah, Sutherland, Judy, Thakur, Vibha, Westfall, Kristen, Wood, Susanna A., Wright, Michael, Zhang, Guang, Pochon, Xavier

“… However, variance in laboratory procedures, analytical workflows and bioinformatic pipelines impede the transferability and comparability of results across research groups…”
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A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry by Ahrens, Christian H, Wade, Joseph T, Champion, Matthew M, Langer, Julian D

“…Small proteins of up to ∼50 amino acids are an abundant class of biomolecules across all domains of life. Yet due to the challenges inherent in their size,…”
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A proof‐of‐concept study of an automated solution for clinical metagenomic next‐generation sequencing by Luan, Y., Hu, H., Liu, C., Chen, B., Liu, X., Xu, Y., Luo, X., Chen, J., Ye, B., Huang, F., Wang, J., Duan, C.

“…Aims Metagenomic next‐generation sequencing (mNGS) has been utilized for diagnosing infectious diseases. It is a culture‐free and hypothesis‐free nucleic acid…”
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Advances in molecular tools for parasitic nematodes of animals – From genetic markers to metabarcoding and genomics by Gasser, Robin B.

“…Parasitic nematodes are globally important pathogens of animals, humans and plants. The accurate identification and characterisation of these nematodes are…”
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Appyters: Turning Jupyter Notebooks into data-driven web apps by Clarke, Daniel J.B., Jeon, Minji, Stein, Daniel J., Moiseyev, Nicole, Kropiwnicki, Eryk, Dai, Charles, Xie, Zhuorui, Wojciechowicz, Megan L., Litz, Skylar, Hom, Jason, Evangelista, John Erol, Goldman, Lucas, Zhang, Serena, Yoon, Christine, Ahamed, Tahmid, Bhuiyan, Samantha, Cheng, Minxuan, Karam, Julie, Jagodnik, Kathleen M., Shu, Ingrid, Lachmann, Alexander, Ayling, Sam, Jenkins, Sherry L., Ma'ayan, Avi

“… Appyters were used to create many bioinformatics web-based reusable workflows, including applications to build customized machine learning pipelines, analyze…”
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Misdetection of frameshifts in SARS-CoV-2 genomes: need for additional harmonisation and efficient monitoring of data workflows by Kogoj, Rok, Petrillo, Mauro, Zakotnik, Samo, Suljič, Alen, Korva, Miša, Leoni, Gabriele

“… During the pandemic, several bioinformatics pipelines and workflows have been developed to streamline analysis, shorten turnaround time and ensure reproducibility…”
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Diazotroph Community Characterization via a High-Throughput nifH Amplicon Sequencing and Analysis Pipeline by Gaby, John Christian, Rishishwar, Lavanya, Valderrama-Aguirre, Lina C, Green, Stefan J, Valderrama-Aguirre, Augusto, Jordan, I King, Kostka, Joel E

“… In this study, we advance the state of the art for analysis by evaluating primer set performance, developing an improved amplicon sequencing workflow, and implementing a user-friendly bioinformatics pipeline…”
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Integrating AI and CRISPR Cas13a for rapid detection of tomato brown rugose fruit virus by Karimi, Marzieh, Ghorbani, Abozar, Niazi, Ali, Rostami, Mahsa, Tahmasebi, Ahmad

“… Integrating bioinformatic…”
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TaME-seq2: tagmentation-assisted multiplex PCR enrichment sequencing for viral genomic profiling by Hesselberg Løvestad, Alexander, Stosic, Milan S., Costanzi, Jean-Marc, Christiansen, Irene Kraus, Aamot, Hege Vangstein, Ambur, Ole Herman, Rounge, Trine B.

“… (HPV16, 18, 31, 33, and 45). Here, we present TaME-seq2 with an updated laboratory workflow and bioinformatics pipeline…”
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PASTMUS: mapping functional elements at single amino acid resolution in human cells by Zhang, Xinyi, Yue, Di, Wang, Yinan, Zhou, Yuexin, Liu, Ying, Qiu, Yeting, Tian, Feng, Yu, Ying, Zhou, Zhuo, Wei, Wensheng

“…), which provides a streamlined workflow and a bioinformatics pipeline to identify critical amino acids of proteins in their native biological contexts…”
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MicrobiomeStatPlots: Microbiome statistics plotting gallery for meta‐omics and bioinformatics by Bai, Defeng, Ma, Chuang, Xun, Jiani, Luo, Hao, Yang, Haifei, Lyu, Hujie, Zhu, Zhihao, Gai, Anran, Yousuf, Salsabeel, Peng, Kai, Xu, Shanshan, Gao, Yunyun, Wang, Yao, Liu, Yong‐Xin

“… This platform integrates essential bioinformatics workflows with multi‐omics pipelines and provides 82 distinct visualization cases for interpreting microbiome datasets…”
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