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/or annotations (from raw files or Refseq IDs), and runs commonly used tools to assess their quality.
There are different ways you can run this pipeline. 1. Genome only, 2. Annotation only, or 3. Genome and Annotation.
Genome Only:
[NCBIGENOMEDOWNLOAD]
- Or you provide your own genomes[BUSCO_BUSCO]
: Determines how complete is the genome compared to expected.
2b. [QUAST]
: Determines the N50, how contiguous the genome is.
2c. More optionsGenome and Annnotation:
[NCBIGENOMEDOWNLOAD]
- Or you provide your own genomes/annotations[BUSCO_BUSCO]
: Determines how complete is the genome compared to expected.
2b. [QUAST]
: Determines the N50, how contiguous the genome is.
2c. More options[AGAT]
: Gene, feature, length, averages, counts. [GFFREAD]
.[ORTHOFINDER_CAFE]
.Annnotation Only:
[NCBIGENOMEDOWNLOAD]
- Or you provide your own annotations.[AGAT]
: Gene, feature, length, averages, counts.[!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:
sample,genome.fasta,annotation.gff
Homo_sapiens,/path/to/genome.fasta,/path/to/annotation.gff3
Gorilla_gorilla,/path/to/genome.fasta,
Pan_paniscus,,/path/to/annotation.gff3
Or to Refseq IDs of your species:
sample,refseqID
Pongo_abelii,GCF_028885655.2
Macaca_mulatta,GCF_003339765.1
You can mix the two input types. Also, notice you can leave the genome or annotation absent.
Each row represents a species, with its associated genome, gff or Refseq ID (to autodownload the genome + gff).
Now, you can run the pipeline using:
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.
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:
If you would like to contribute to this pipeline, please see the contributing guidelines.
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.