Workflows
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Tool
BLAST1
BRAKER11
BUSCO1
fastp1
FastQC1
funannotate1
Minimap21
MultiQC1
protexcluder1
RepeatMasker1
RepeatModeler1
STAR1
StringTie1
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3
Workflows visible to you, out of a total of 3
Work-in-progress
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 ...
Work-in-progress
GALOP - Genome Assembly using Long reads Pipeline
This repository contains an exact copy of the standard Genoscope long reads assembly pipeline.
At the moment, this is not intended for users to download as it uses grid submission commands that will only work at Genoscope. As time goes on, we intend to make this pipeline available to a broader audience. However, genome assembly and polishing commands are accessible in the lib/assembly.py
and lib/polishing.py
files.
galop.py -h
Mandatory
...
Stable