https://github.com/barbarahelena/saltprofiler

https://github.com/barbarahelena/saltprofiler

Repository

https://github.com/barbarahelena/saltprofiler/blob/master/

  


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## Introduction

**saltprofiler** is a bioinformatics pipeline for assembly, binning and annotation of metagenomes focused on salt tolerance genes. The pipeline is based on the nf-core mag pipeline.



## Pipeline summary

This pipeline uses paired-end short-read fastq files (with or without assemblies) as input, quality trims the reads and adapters with [fastp](https://github.com/OpenGene/fastp) and [Porechop](https://github.com/rrwick/Porechop), and performs basic QC with [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and merge multiple sequencing runs.

The pipeline then:
- assigns taxonomy to reads using [Centrifuge](https://ccb.jhu.edu/software/centrifuge/) and/or [Kraken2](https://github.com/DerrickWood/kraken2/wiki)
- performs assembly using [SPAdes](http://cab.spbu.ru/software/spades/), and checks their quality using [Quast](http://quast.sourceforge.net/quast)
- performs metagenome binning using [MetaBAT2](https://bitbucket.org/berkeleylab/metabat/src/master/), [MaxBin2](https://sourceforge.net/projects/maxbin2/), and checks the quality of the genome bins using [Busco](https://busco.ezlab.org/), or [CheckM](https://ecogenomics.github.io/CheckM/).
- predicts protein-coding genes for the assemblies using [Prodigal](https://github.com/hyattpd/Prodigal), and bins with [Prokka](https://github.com/tseemann/prokka)
- assigns taxonomy to bins using [GTDB-Tk](https://github.com/Ecogenomics/GTDBTk) and/or [CAT](https://github.com/dutilh/CAT)

Furthermore, the pipeline creates various reports in the results directory specified, including a [MultiQC](https://multiqc.info/) report summarizing some of the findings and software versions.

## 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.

> [!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).

For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/mag/usage) and the [parameter documentation](https://nf-co.re/mag/parameters).

## Pipeline output

To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/mag/results) tab on the nf-core website pipeline page.
For more details about the output files and reports, please refer to the
[output documentation]().

### Group-wise co-assembly and co-abundance computation

Each sample has an associated group ID (see [input specifications](https://nf-co.re/mag/usage#input_specifications)). This group information can be used for group-wise co-assembly with `MEGAHIT` or `SPAdes` and/or to compute co-abundances for the binning step with `MetaBAT2`. By default, group-wise co-assembly is disabled, while the computation of group-wise co-abundances is enabled. For more information about how this group information can be used see the documentation for the parameters [`--coassemble_group`](https://nf-co.re/mag/parameters#coassemble_group) and [`--binning_map_mode`]().

When group-wise co-assembly is enabled, `SPAdes` is run on accordingly pooled read files, since `metaSPAdes` does not yet allow the input of multiple samples or libraries. In contrast, `MEGAHIT` is run for each group while supplying lists of the individual readfiles.

## Credits

The salt tolerance-specific modules were written by Barbara, but most of the pipeline is based on the nf-core/mag pipeline. This pipeline was written by [Hadrien Gourl](https://hadriengourle.com) at [SLU](https://slu.se), [Daniel Straub](https://github.com/d4straub) and [Sabrina Krakau](https://github.com/skrakau) at the [Quantitative Biology Center (QBiC)](http://qbic.life). [James A. Fellows Yates](https://github.com/jfy133) and [Maxime Borry](https://github.com/maxibor) at the [Max Planck Institute for Evolutionary Anthropology](https://www.eva.mpg.de) joined in version 2.2.0.

## Citations

If you use this pipeline, I suggest that you cite the nf-core/mag preprint, since most of this pipeline is based on their work:

> **nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning**
>
> Sabrina Krakau, Daniel Straub, Hadrien Gourl, Gisela Gabernet, Sven Nahnsen.
>
> NAR Genom Bioinform. 2022 Feb 2;4(1):lqac007. doi: [10.1093/nargab/lqac007](https://doi.org/10.1093/nargab/lqac007).

Additionally you can cite the pipeline directly with the following doi: [10.5281/zenodo.3589527](https://doi.org/10.5281/zenodo.3589527)

An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](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](https://dx.doi.org/10.1038/s41587-020-0439-x).

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