Introduction

sanger-tol/genomeassembly is a bioinformatics pipeline for de-novo genome assembly from long read data (PacBio HiFi or ONT), long-range Hi-C data, and optionally Illumina WGS and Illumina 10X linked reads. It is capable of producing primary/alternative assembles, Hi-C phased assemblies using Hi-C data, and trio-binned assemblies using Illumina WGS data from parental sequencing.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!

On release, automated continuous integration tests run the pipeline on a full-sized dataset on the LSF infrastructure. This ensures that the pipeline runs on LSF, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.

Pipeline summary

1. If FastK databases and coverage information information are not provided, the pipeline first builds these and estimates the genome coverage using genomescope2.
2. Assembles the provided long reads using hifiasm, optionally producing hic-phased or trio-binned assemblies.
3. (optional) Purges retained haplotigs from the assembly using purge_dups.
4. (optional) Polishes the combined assembly using Illumina 10X reads with Longranger and Freebayes
5. Maps Hi-C reads to each assembly using bwamem2 or minimap2.
6. Scaffolds each assembly using long-range Hi-C interactions using YaHS.
7. Produces numerical statistics for each assembly at each stage of the pipeline using GFASTATS (assembly statiscics), BUSCO (single-copy ortholog statistics), and MERQURY.FK (QV and kmer-completeness).
8. Assembles organelles using de-novo assembly oatk and reference-based assembly MitoHiFi.

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.

Currently, it is advised to run the pipeline with docker or singularity as some modules do not have a conda env associated with them.

Now, you can run the pipeline using:

nextflow run sanger-tol/genomeassembly \
   -profile <docker/singularity/.../institute> \
   --input input.yaml \
   --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

sanger-tol/genomeassembly was originally written by Ksenia Krashennikova and Jim Downie.

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

@priyanka-surana for the code review, very helpful coding suggestions, and assistance with pushing this pipeline forward through development.

@mcshane and @c-zhou for the design and implementation of the original pipelines for purging (@mcshane), polishing (@mcshane) and scaffolding (@c-zhou).

TreeVal team Damon-Lee Pointon (@DLBPointon), Yumi Sims (@yumisims) and William Eagles (@weaglesBio) for implementation of the hic-mapping pipeline.

@muffato for help with nf-core integration, dealing with infrastructure and troubleshooting, for the code reviews and valuable suggestions at the different stages of the pipeline development.

@gq1 for the code review, valuable suggestions to the code improvement and contributions to the full test setup.

@mahesh-panchal for nextflow implementation of the purging pipeline, code review and valuable suggestions to the nf-core modules implementation.

Contributions and Support

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

Citations

If you use sanger-tol/genomeassembly for your analysis, please cite it using the following doi: 10.5281/zenodo.10391851.

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.