Workflows

This workflow takes a collection of BAM (output of STAR) and a gtf. It extends the input gtf using de novo annotation.

Annotation of an assembled bacterial genomes to detect genes, potential plasmids, integrons and Insertion sequence (IS) elements.

Antimicrobial resistance gene detection from assembled bacterial genomes

Importing single-end multiplexed data (not demultiplexed yet)

Use DADA2 for sequence quality control. DADA2 is a pipeline for detecting and correcting (where possible) Illumina amplicon sequence data. As implemented in the q2-dada2 plugin, this quality control process will additionally filter any phiX reads (commonly present in marker gene Illumina sequence data) that are identified in the sequencing data, and will filter chimeric sequences.

dada2 amplicon analysis for paired end data

The workflow has three main outputs:

• the sequence table (output of makeSequenceTable)
• the taxonomy (output of assignTaxonomy)
• the counts which allow to track the number of sequences in the samples through the steps (output of sequence counts)

This workflow performs segmentation and counting of cell nuclei using fluorescence microscopy images. The segmentation step is performed using Otsu thresholding (Otsu, 1979). The workflow is based on the tutorial: https://training.galaxyproject.org/training-material/topics/imaging/tutorials/imaging-introduction/tutorial.html

Assemble long reads with Flye, then view assembly statistics and assembly graph

Run velocyto to get loom with counts of spliced and unspliced. It will extract the 'barcodes' from the bundled outputs.