https://github.com/robsyme/nextflow-annotate

Workflows I find helpful for fungal genome annotation
https://github.com/robsyme/nextflow-annotate

Last synced: 24 days ago
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Workflows I find helpful for fungal genome annotation

• Host: GitHub
• URL: https://github.com/robsyme/nextflow-annotate
• Owner: robsyme
• License: mit
• Created: 2014-10-01T20:08:34.000Z (about 10 years ago)
• Default Branch: master
• Last Pushed: 2018-05-02T01:52:51.000Z (over 6 years ago)
• Last Synced: 2023-04-10T14:49:23.895Z (over 1 year ago)
• Language: Perl
• Homepage:
• Size: 848 KB
• Stars: 20
• Watchers: 3
• Forks: 11
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# nextflow-annotate

This is a push to gather together some tools that are helpful for

genome annotation, and serve as a forkable, version-controlled,

reusable, and citable record of our pipeline. The steps use nextflow

as a workflow engine so we can abstract the individual steps from

their execution environment (SGE, MPI or simple local multithreading).

This is not a push-button solution, but it can serve as a starting

point for annotating your new genome.

## Prerequisites

The minimum prerequisites are [docker](http://docker.io) and

[nextflow](http://nextflow.io), and a fasta file (henceforth

`scaffolds.fasta`) of your genome assembly.

Some steps require software or data with licences that restrict

distribution, but I've kept them to a minimum and will make it clear

when those pieces are necessary.

## Steps

Each of these steps corresponds to one of the nextflow recipes

provided by this repository.

### Transposon Identification

Taking cues from [jamg](http://jamg.sourceforge.net), we transcribe

all of the open reading frames and then use hhblit to match against a

database of known transposons. A GFF file is produced that describes

to position of the transposons that we find.

This uses two docker images, which will be pulled automatically from

the docker registry as needed.

### Finding Repeats

Repeats are an important part of the final genome annotation. I

recommend a two-step process:

1. Find denovo repeats with RepeatScout.

2. Use the RepeatScout output in conjuctions with the latest RepBase

library as input to RepeatMasker

I've taken care of the RepeatScout and RepeatMasker installation by

bundling them as docker images. The only hiccup is that RepBase

requires registration.