DENOVOSEQ - PIPELINE MODE USAGE


6.1 - CONFIGURING AND RUNNING PIPELINES

The pipeline mode of DeNovoSeq is a pipeline configuration system that let the user to execute all the steps of a pipeline, automatically one after the other. To perform a de novo analysis using the pipeline mode, the user must access the DeNovo protocols tab of the Top menu and then select the option Pipeline Mode. Then a first pipeline interface will appear summarizing all currently available pipelines based on Command Line Interface (CLI) software offered by the Pipeline mode of DeNovoSeq.

There are three available types of pipelines;

  1. Genome & Transcriptome DeNovo assembly.
  2. Augustus-based Gene Prediction
  3. NCBI-Blast-based Annotation

To perform an analysis using the pipeline mode, please go to [ Transcripts Protocols → Pipeline Mode ] and follow Fig. 26

Figure 26

Figure 26: Example of configuration and execution for a RNA-seq analysis using the pipeline mode.

Using the pipeline mode you only need to select one pipeline from the list and then configure the experiment going to a set of nested interfaces to;

  1. 1. upload any input data or material needed by the pipeline (i.e. fastq files, input data configuration.
  2. declare the outputs
  3. configure the parameters and options of each CLI tool used in each step.
  4. finally run the pipeline .









GPRO licensing and Usage           Former versions           TSI-100903-2019-11

Biotechvana


Valencia Lab
Parc Cientific Universitat de Valencia
Carrer del Catedràtic Agustín Escardino, 9. 46980 Paterna (Valencia) Spain
Madrid Lab
Parque Científico de Madrid
Campus de Cantoblanco
Calle Faraday 7, 28049 Madrid Spain
Contact us
Phone: +34 960 06 74 93
Email: biotechvana@biotechvana.com

Supported by


Hipra Scientific S.L.U, Polypeptide Therapeutic Solutions S.L., Biotechvana S.L. and Nostrum Biodiscovery constitute the consortium of enterprises participating in the project "Research of a new vaccine for a human respiratory disease", granted by the CDTI (Center for Industrial Technological Development), and supported by the Ministry of Science and Innovation and financed by the European Union – NextGenerationEU. The main objective of this project is to design a safe immunogenic and effective vaccine against the respiratory syncytial virus.

Biotechvana © 2015
Privacy policy
Política de privacidad
This website use cookies, by continuing to browse the site you are agreeing to our use of cookies. More info about our cookies here.