Introduction

sanger-tol/insdcdownload is a pipeline that downloads assemblies from INSDC into a Tree of Life directory structure.

The pipeline takes an assembly accession number, as well as the assembly name, and downloads it. It also builds a set of common indices (such as samtools faidx), and extracts the repeat-masking performed by the NCBI.

Steps involved:

• Download from the NCBI the genomic sequence (Fasta) and the assembly stats and reports files.
• Turn the masked Fasta file into an unmasked one.
• Compress and index all Fasta files with bgzip, samtools faidx, and samtools dict.
• Generate the .sizes file usually required for conversion of data files to UCSC's "big" formats, e.g. bigBed.
• Extract the coordinates of the masked regions into a BED file.
• Compress and index the BED file with bgzip and tabix.

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.

The easiest is to provide the exact name and accession number of the assembly like this:

nextflow run sanger-tol/insdcdownload --assembly_accession GCA_927399515.1 --assembly_name gfLaeSulp1.1

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.

The pipeline also supports bulk downloads through a sample-sheet. More information about this mode on our pipeline website.

Credits

sanger-tol/insdcdownload was mainly written by Matthieu Muffato, with major borrowings from a's read-mapping pipeline, e.g. the script to remove the repeat-masking, and the overall structure and layout of the sub-workflows.

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

• Priyanka Surana for providing reviews.
• Tyler Chafin for updates and maintenance.

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 #pipelines channel. Please create an issue on GitHub if you are not on the Sanger slack channel.

Citations

If you use sanger-tol/insdcdownload for your analysis, please cite it using the following doi: 10.5281/zenodo.6983932

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.