nf-core/genomeassembler

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Introduction

nf-core/genomeassembler is a bioinformatics pipeline that carries out genome assembly, polishing and scaffolding from long reads (ONT or pacbio). Assembly can be done via flye or hifiasm, polishing can be carried out with medaka (ONT), or pilon (requires short-reads), and scaffolding can be done using LINKS, Longstitch, or RagTag (if a reference is available). Quality control includes BUSCO, QUAST and merqury (requires short-reads). Currently, this pipeline does not implement phasing of polyploid genomes or HiC scaffolding.

Usage

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

sample,ontreads,hifireads,ref_fasta,ref_gff,shortread_F,shortread_R,paired
sampleName,ontreads.fa.gz,hifireads.fa.gz,assembly.fasta.gz,reference.fasta,reference.gff,short_F1.fastq,short_F2.fastq,true

Each row represents one genome to be assembled. sample should contain the name of the sample, ontreads should contain a path to ONT reads (fastq.gz), hifireads a path to HiFi reads (fastq.gz), ref_fasta and ref_gff contain reference genome fasta and annotations. shortread_F and shortread_R contain paths to short-read data, paired indicates if short-reads are paired. Columns can be omitted if they contain no data, with the exception of shortread_R, which needs to be present if shortread_F is there, even if it is empty.

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Now, you can run the pipeline using:

nextflow run nf-core/genomeassembler \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR>

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 tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.

Credits

nf-core/genomeassembler was originally written by Niklas Schandry (@nschan).

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

• Mahesh Binzer-Panchal (@mahesh-panchal)
• Matthias Hörtenhuber (@mashehu)
• Daniel Straub (@d4straub)

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 #genomeassembler 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.