Workflows
What is a Workflow?Filters
AnnoAudit - Annotation Auditor
AnnoAudit is a robust Nextflow pipeline designed to evaluate the quality of genomic annotations through a multifaceted approach.
Overview of the workflow
The workflow assess the annotation quality based on different criteria:
- Protein evidence support
- RNASeq evidence support
- Statistics of the predictions (i.e., gene length, exon number, etc.)
- Ortholog analysis (BUSCO, OMArk)
Input data
- Reference genome
genome.[.fna, .fa, .fasta]
- Annotation ...
Prostate cancer classification workflow
This workflow segments tissue regions and classifies prostate cancer on H&E whole slide images, using AI. It consists of three steps:
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low-resolution tissue segmentation to select areas for further processing;
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high-resolution tissue segmentation to refine borders - it uses step 1 as input;
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high-resolution normal/cancer classification - it uses step 1 as input.
Tissue segmentation workflow
This workflow performs tissue segmentation on H&E whole slide images using AI.
This workflow perform the scaffolding of a genome assemble using HiC data with YAHS. Part of the VGP set of workflows.
This workflow generates Hi-C contact maps for genome assemblies in the Pretext format. It is compatible with one or 2 haplotypes. It includes tracks for PacBio read coverage, Gaps, and telomeres. The Pretext files can be open in PretextView for the manual curation of genome assemblies.
Genome Assembly with Hifi reads and Trio Data
Generate phased assembly based on PacBio Hifi Reads using parental Illumina data for phasing. Part of the VGP workflow suite, it needs to be run after the Trio k-mer Profiling workflow VGP2.
Inputs
- Hifi long reads [fastq]
- Concatenated Illumina reads : Paternal [fastq]
- Concatenated Illumina reads : Maternal [fastq]
- K-mer database [meryldb] generated by VGP2 workflow.
- Paternal hapmer database [meryldb] generated by VGP2 workflow.
...
Purge contigs marked as duplicates by purge_dups (could be haplotypic duplication or overlap duplication). This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5)