Workflows
What is a Workflow?Filters
Galaxy version of pre-processing of reads from COVID-19 samples. QC + human read cleaning Based on https://github.com/Finn-Lab/Metagen-FastQC/blob/master/metagen-fastqc.sh
CWL version of the md_list.cwl workflow for HPC.
Workflow to build different indices for different tools from a genome and transcriptome.
This workflow expects an (annotated) genome in GBOL ttl format.
Steps:
- SAPP: rdf2gtf (genome fasta)
- SAPP: rdf2fasta (transcripts fasta)
- STAR index (Optional for Eukaryotic origin)
- bowtie2 index
- kallisto index
Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures
Type: Scipion
Creators: Carlos Oscar Sorzano Sanchez, Roberto Melero, Marta Martinez
Submitter: Laura del Cano
Scipion is a workflow engine mostly for Cryo-Electron Microscopy image processing. In this extremely simple workflow, we load the Relion 3.0 tutorial data and process it to 2.9A resolution.
This WF is based on the official Covid19-Galaxy assembly workflow as available from https://covid19.galaxyproject.org/genomics/2-assembly/ . It has been adapted to suit the needs of the analysis of metagenomics sequencing data. Prior to be submitted to INDSC databases, these data need to be cleaned from contaminant reads, including reads of possible human origin.
The assembly of the SARS-CoV-2 genome is performed using both the Unicycler and the SPAdes assemblers, similar to the original WV.
To ...
RNA-RNA interactome analysis using ChiRA tools suite. The aligner used is CLAN.
RNA-RNA interactome analysis using ChiRA tools suite. The aligner used is BWA-MEM.
Abstract CWL Automatically generated from the Galaxy workflow file: CLM-FATES_ ALP1 simulation (5 years)
metaboigniter is bioinformatics pipeline for pre-processing of mass spectrometry-based metabolomics data. It can be used to perform quantification and identification based on MS1 and MS2 data. The backbone of pipeline is based on XCMS, OpenMS, CAMERA, MSnbase, MetFrag, CSIFingerID, CFM-ID, and several other customized tools to noise filtering, quantification and identification both for library and in-silico identification. Please go on to this page to learn how to use the workflow
The pipeline ...