Workflows
What is a Workflow?Filters
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 ...
Genome assembly: Unicycler-based WF for Klebsiella pneumoniae [Wick et al. Microbial genomics 2017]
Genome assembly: Flye-based WF for highly repetitive genomes [Schmid et al. NAR 2018]
Basic workflows inspired by the Nanopolish tutorials
Galaxy-E (ecology.usegalaxy.eu) workflow to calculate species presence / absence, community metrics and compute generalized linear models to identify effects and significativity of these effects on biodiversity.