Workflows

Clinical Metaproteomics 4: Quantitation

This workflow takes as input SR BAM from ChIP-seq. It calls peaks on each replicate and intersect them. In parallel, each BAM is subsetted to smallest number of reads. Peaks are called using all subsets combined. Only peaks called using a combination of all subsets which have summits intersecting the intersection of at least x replicates will be kept.

This workflow processes the CMO fastqs with CITE-seq-Count and include the translation step required for cellPlex processing. In parallel it processes the Gene Expresion fastqs with STARsolo, filter cells with DropletUtils and reformat all outputs to be easily used by the function 'Read10X' from Seurat.

Scaffolding using HiC data with YAHS.

A workflow for the analysis of pox virus genomes sequenced as half-genomes (for ITR resolution) in a tiled-amplicon approach

Automated inference of stable isotope incorporation rates in proteins for functional metaproteomics

Generate Nx and Size plot for multiple assemblies

Inputs

Collection of fasta files. The name of each item in the collection will be used as label for the Nx and Size plots.

Outputs

1. Nx plot
2. Size plot

This workflow takes as input a SRA_manifest from SRA Run Selector and will generate one fastq file or fastq pair of file for each experiment (concatenated multiple runs if necessary). Output will be relabelled to match the column specified by the user.

Antimicrobial resistance gene detection from assembled bacterial genomes

Assembly of bacterial paired-end short read data with generation of quality metrics and reports