<img alt="nf-core/assemblyeval" src="docs/images/nf-core-assemblyeval_logo_light.png">

Introduction

nf-core/assemblyeval is a bioinformatics pipeline that applies the four C’s genome assembly quality check procedure evaluating contamination, contiguity, completeness and correctness. Furthermore, due to errors that can be introduced by the sequencing technology or the assembly tool used, it is important at the end of pipeline’s run to inspect more assertively candidate misjoined regions. Therefore, in addition to producing a detailed comparative report showing numerous metrics and graphics evaluating the quality of the assemblies, the pipeline provides an interactive report showing candidate assembly errors at the single-nucleotide level.

1. Read QC (FastQC)
2. Removal of contaminants (Optional):
   1. Removal of adptor/vector contaminants ([FCS-adaptor])
   2. Removal of genome contaminants ([FCS-GX])
   3. Generate a clean assembly excluding contaminants ([FCS-CLEAN])
3. Module
4. TO DO

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 file with your input data that looks like file assets/chla_test_input_channels.yaml:

samples:
  - metadata:
      id: Ctrachomatis
      kmer_size: 21
      ploidy: 1
      # Organism domain: either euk or prok
      organism_domain: prok
      taxid: "315277" 
      busco_lineages:
        - "chlamydiae_odb10"
    assembly:
      - id: ref
        pri_asm: "./data_test/GCF_000012125.1_ASM1212v1_genomic.fasta"
      - id: ctracho_5inversions_default
        pri_asm: "./data_test/ctracho_5inversions_default.simseq.genome.fa"
      - id: ctracho_10persnp_default
        pri_asm: "./data_test/ctracho_10persnp_default.simseq.genome.fa"
      - id: ctracho_5inversions_split
        pri_asm: "./data_test/Ctrachomatis_ctracho_5inversions_default_cleaned_breaked.fasta"
    illumina:
      - read1: "./data_test/mason_R1_001.fastq.gz"
        read2: "./data_test/mason_R2_001.fastq.gz"

Each row in assembly section represents an assembly obtained from a different genome assembler tool. The section illumina indicates a pair of fastq files (paired end) used to validate the assembly.

Now, you can test the pipeline using:

nextflow run main.nf \
   -profile docker,test \
   --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.

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

To see the results of an example test run with a full size dataset refer to the results and the IGV report.

After the pipeline finishes, the main outputs are self-contained HTML located at /multiqc/ and /igvreport/.

For more details about the output files and reports, please refer to the output documentation.

Credits

nf-core/assemblyeval was originally written by Rodrigo Theodoro Rocha.

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.

For further information or help, don't hesitate to get in touch on the Slack #assemblyeval channel (you can join with this invite).

Citations

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

You can cite the nf-core publication as follows:

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.