Introduction

nf-core/kmerseek is a bioinformatics pipeline that, like BLAST, searches for similar sequences using a query in a database, but unlike BLAST, uses protein k-mers. The goal is to find proteins of similar function.

1. Converts protein sequences into k-mer signatures (Sourmash)
2. [TODO] Searches query signature in target (Sourmash)
3. [TODO] Uses custom code to identify statistically significant matches
4. [TODO] Uses custom code to show matching k-mer sequences
5. Present QC for raw reads (MultiQC)

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 samplesheet with your input data that looks as follows:

sample,fasta
snap25a,snap25a_mxe_exon.fa
snap25b,snap2ba_mxe_exon.fa.gz

Each row represents a single query protein sequence as a fasta file.

Now, you can run the pipeline using:

nextflow run nf-core/kmerseek \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --fasta uniref50.fa.gz \
   --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.

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/kmerseek was originally written by Olga Botvinnik.

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 #kmerseek 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.