Workflows
What is a Workflow?Filters
The workflow for Illumina-sequenced ARTIC data builds on the RNASeq workflow for paired-end data using the same steps for mapping and variant calling, but adds extra logic for trimming ARTIC primer sequences off reads with the ivar package. In addition, this workflow uses ivar also to identify amplicons affected by ARTIC primer-binding site mutations and tries to exclude reads derived from such tainted amplicons when calculating allele-frequencies of other variants.
Automated inference of stable isotope incorporation rates in proteins for functional metaproteomics
Run baredSC in 1 dimension in logNorm for 1 to N gaussians and combine models.
VGP Workflow #1
This workflow produces a Meryl database and Genomescope outputs that will be used to determine parameters for following workflows, and assess the quality of genome assemblies. Specifically, it provides information about the genomic complexity, such as the genome size and levels of heterozygosity and repeat content, as well about the data quality.
Inputs
- A collection of Hifi long reads in FASTQ format
- k-mer length
- Ploidy
Outputs
- Meryl Database of kmer counts
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Create Meryl Database used for the estimation of assembly parameters and quality control with Merqury. Part of the VGP pipeline.
This workflow is composed with the XCMS tool R package (Smith, C.A. 2006) able to extract, filter, align and fill gapand the possibility to annotate isotopes, adducts and fragments using the CAMERA R package (Kuhl, C 2012).
This workflow is composed with the XCMS tool R package (Smith, C.A. 2006) able to extract and the metaMS R package (Wehrens, R 2014) for the field of untargeted metabolomics.
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.
Type: Galaxy
Creators: Lucille Delisle, Mehmet Tekman, Hans-Rudolf Hotz, Daniel Blankenberg, Wendi Bacon
Submitter: WorkflowHub Bot
Run velocyto to get loom with counts of spliced and unspliced. It will extract the 'barcodes' from the bundled outputs.