https://github.com/aginnimb/genome_sequence_similarity

Nextflow pipeline to perform sequence similarity between two genomes using ANI calculation

https://github.com/aginnimb/genome_sequence_similarity

Repository

Nextflow pipeline to perform sequence similarity between two genomes using ANI calculation

https://github.com/aginnimb/genome_sequence_similarity/blob/main/

## Introduction

**sequencesim/sequencesimilarity** is a bioinformatics pipeline that ...






1. Whole genome average nucleotide identity ([`fastANI`](https://github.com/ParBLiSS/FastANI))
2. Whole Genome MLST analysis ([`EToKi`](https://github.com/zheminzhou/EToKi))
3. Present QC for genomes and results ([`MultiQC`](http://multiqc.info/))

## Usage

> [!NOTE]
> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.



Now, you can run the pipeline using:



```bash
nextflow run main.nf \
   -profile  \
   --input fasta_samplesheet.csv \
   --reference_fastas 
   --platform illumina
   --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](https://nf-co.re/usage/configuration#custom-configuration-files).

## Credits

sequencesim/sequencesimilarity was originally written by SMorrison42 and Aginnimb.

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](.github/CONTRIBUTING.md).

## Citations






An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.

This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/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](https://dx.doi.org/10.1038/s41587-020-0439-x).

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