CWL4IncorporateTSSintoGXF

This workflow determines TSS based on the analysis of CAGE-seq data and incorporates TSS information and 5'UTR information calculated based on TSS information into the gene annotation file (gff/gtf). The R package, TSSr, is used to determine TSS.

Requirements

• cwltool

Install using pip

pip install cwltool 

Install using conda

conda create -n cwltool 
conda activate
...

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

score-assemblies

A Snakemake-wrapper for evaluating de novo bacterial genome assemblies, e.g. from Oxford Nanopore (ONT) or Illumina sequencing.

The workflow includes the following programs:

• pomoxis assess_assembly and assess_homopolymers
• dnadiff from the mummer package
• NucDiff
• QUAST
• BUSCO

...

Functional annotation of protein sequences

Structural and functional genome annotation with Funannotate

Masking repeats in a genome using RepeatMasker

Refining Genome Annotations with Apollo