Workflows

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224 Workflows visible to you, out of a total of 237

HiFi de novo genome assembly workflow

HiFi-assembly-workflow is a bioinformatics pipeline that can be used to analyse Pacbio CCS reads for de novo genome assembly using PacBio Circular Consensus Sequencing (CCS) reads. This workflow is implemented in Nextflow and has 3 major sections.

Please refer to the following documentation for detailed description of each workflow section:

  • Pre-assembly quality control (QC)
  • Assembly
  • Post-assembly QC

HiFi assembly workflow flowchart

![flow chart ...

Type: Nextflow

Creators: None

Submitter: Naga Kasinadhuni

Workflow Kallisto RNAseq

All tool CWL files and other workflows can be found here: Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl Workflows: https://git.wur.nl/unlock/cwl/-/tree/master/cwl/workflows

The dependencies are either accessible from https://unlock-icat.irods.surfsara.nl (anonymous,anonymous) and/or By using the conda / pip environments as shown in ...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Bart Nijsse

Work-in-progress

A workflow for the quality assessment of mass spectrometry (MS) based proteomics analyses

Type: KNIME

Creator: Julian Uszkoreit

Submitter: Julian Uszkoreit

Stable

Workflow for Illumina paired read quality control, trimming and filtering. Multiple paired datasets will be merged into single paired dataset. Summary:

  • FastQC on raw data files
  • fastp for read quality trimming
  • BBduk for phiX and (optional) rRNA filtering
  • Kraken2 for taxonomic classification of reads (optional)
  • BBmap for (contamination) filtering using given references (optional)
  • FastQC on filtered (merged) data

All tool CWL files and other workflows can be found here: Tools: ...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Bart Nijsse

Stable

StructuralVariants Workflow

Type: Common Workflow Language

Creators: Laura Rodriguez-Navas, Daniel López-López

Submitter: Laura Rodriguez-Navas

Objective. Biomarkers have become important for the prognosis and diagnosis of various diseases. High-throughput methods such as RNA-sequencing facilitate the detection of differentially expressed genes (DEGs), hence potential biomarker candidates. Individual studies suggest long lists of DEGs, hampering the identification of clinically relevant ones. Concerning preeclampsia, a major obstetric burden with high risk for adverse maternal and/or neonatal outcomes, limitations in diagnosis and ...

Type: Galaxy

Creator: Marlene Rezk

Submitter: Marlene Rezk

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