Introduction

ecoflow/genomeqc is a bioinformatics pipeline that compares the quality of multiple genomes, along with their annotations.

The pipeline takes a list of genomes and annotations (from raw files or Refseq IDs), and runs commonly used tools to assess their quality.

There will be three different ways you can run this pipeline. 1. Genome only, 2. Annotation only, or 3. Genome and Annotation. Only Genome plus Annotation is functional

Genome and Annnotation:

1. Downloads the genome and gene annotation files from NCBI [NCBIGENOMEDOWNLOAD] - Or you provide your own genomes/annotations
2. Describes genome assembly: 2a. [BUSCO_BUSCO]: Determines how complete is the genome compared to expected (protein mode). 2b. [QUAST]: Determines the N50, how contiguous the genome is. 2c. More options
3. Describes your annotation : [AGAT]: Gene, feature, length, averages, counts.
4. Extract longest protein fasta sequences [GFFREAD].
5. Finds orthologous genes [ORTHOFINDER].
6. Summary with MulitQC.

Genome Only (in development):

1. Downloads the genome files from NCBI [NCBIGENOMEDOWNLOAD] - Or you provide your own genomes
2. Describes genome assembly: 2a. [BUSCO_BUSCO]: Determines how complete is the genome compared to expected (genome mode). 2b. [QUAST]: Determines the N50, how contiguous the genome is. 2c. More options
3. Summary with MulitQC.

Annnotation Only (in development):

1. Downloads the gene annotation files from NCBI [NCBIGENOMEDOWNLOAD] - Or you provide your own annotations.
2. Describes your annotation : [AGAT]: Gene, feature, length, averages, counts.
3. Summary with MulitQC.

Usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

First, prepare a samplesheet.csv, where your input data points to genomes + or annotations:

species,refseq,fasta,gff
Homo_sapiens,,/path/to/genome.fasta,/path/to/annotation.gff3
Gorilla_gorilla,,/path/to/genome.fasta,
Pan_paniscus,,/path/to/genome.fasta,/path/to/annotation.gff3

Or to Refseq IDs of your species:

species,refseq,fasta,gff
Pongo_abelii,GCF_028885655.2,,
Macaca_mulatta,GCF_003339765.1,,

You can mix the two input types (in development).

Each row represents a species, with its associated genome, gff or Refseq ID (to autodownload the genome + gff).

You can run the pipeline using test profiles or example input samplesheets:

nextflow run main.nf -resume -profile docker,test --outdir results

or

nextflow run main.nf -resume -profile docker --input assets/samplesheet.csv --outdir results

nextflow run ecoflow/genomeqc \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR>

Warning

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Credits

ecoflow/genomeqc was originally written by Chris Wyatt, Fernando Duarte.

We thank the following people for their extensive assistance in the development of this pipeline:

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.