Genome pre-processing pipeline

This is a local pipeline to pre-process downloaded genomes before feeding them to https://github.com/nf-core/pairgenomealign.

What it does:

This pipeline takes genomes as inputs and soft-masks their repeats with the following software:

• tantan
• windowmasker
• repeatmasker

The input of repeatmasker can be any of:

• repeatmodeller (default)
• DFAM
• a custom repeat library.

Repeatmasker and repeatmodeller are run from the same image as the standard nf-core module. But it is possible to pass the URL to an alternative singularity image, for instance to use the latest TE Tools container

It reports the number of masked bases using

bedtools custommodule gfstrmsk gfsttantan gfstwindowmask multiqc pipeline_info repeatmodeler tantan windowmasker

Disclaimer

This is not an official pipeline. This pipeline uses code and infrastructure developed and maintained by the nf-core initative, and 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.

Usage

First make a sample sheet with usual nf-core pipelines.

samplesheet.csv:

sample,fasta
query_1,path-to-query-genome-file-one.fasta.gz
query_2,path-to-query-genome-file-two.fasta.gz

If the input is not compressed then pass the --gzipped_input=false parameter. Note that mixing compressed and uncompressed input is not supported.

Then run the pipeline as usual:

nextflow run oist/LuscombeU_pairgenomealign-preprocess \
   -profile oist \
   --input samplesheet.csv \
   --outdir <OUTDIR>

Test the dev branch of the pipeline (adapt the -w option for your own case!

nextflow run oist/LuscombeU_pairgenomealign-preprocess -r dev \
   -profile oist,test \
   -w /flash/LuscombeU/`whoami`/cache/deletemeTest \
   --outdir results_test

Test the local checkout

nextflow run ./main.nf \
   -profile oist,test \
   -w /flash/LuscombeU/`whoami`/cache/deletemeTest \
   --outdir results_test

Options

• Point --repeatlib to a FASTA file to have an extra RepeatMasker run using it as a library.
• Set --taxon to a taxon name to have an extra RepeatMasker run using the -species option set to that taxon.
• Point --singularity_image to a local file path like /flash/LuscombeU/singularity.cacheDir/tetools_1.88.5.sif or an URL to singularity image to replace the default one.
• Set the --gzipped_input=false parameter when the input is not compressed..

Pipeline output

tantan

• Masked genome file (TODO: compress it)
• BED file representing the masked regions.

windowmasker

• Masked genome file (TODO: compress it)
• BED file representing the masked regions.
• ustat output file (TODO: remove it)

Credits

nf-core/pairgenomealignmask was originally written by Mahdi.