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.
This pipeline uses paired-end short-read fastq files (with or without assemblies) as input, quality trims the reads and adapters with fastp and Porechop, and performs basic QC with FastQC, and merge multiple sequencing runs.
The pipeline then:
- assigns taxonomy to reads using Centrifuge and/or Kraken2
- performs assembly using SPAdes, and checks their quality using Quast
- performs metagenome binning using MetaBAT2, MaxBin2, and checks the quality of the genome bins using Busco, or CheckM.
- predicts protein-coding genes for the assemblies using Prodigal, and bins with Prokka
- assigns taxonomy to bins using GTDB-Tk and/or CAT
Furthermore, the pipeline creates various reports in the results directory specified, including a MultiQC report summarizing some of the findings and software versions.
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.
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.
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.
Each sample has an associated group ID (see 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 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.
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 Gourlé at SLU, Daniel Straub and Sabrina Krakau at the Quantitative Biology Center (QBiC). James A. Fellows Yates and Maxime Borry at the Max Planck Institute for Evolutionary Anthropology joined in version 2.2.0.
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 Gourlé, Gisela Gabernet, Sven Nahnsen.
NAR Genom Bioinform. 2022 Feb 2;4(1):lqac007. doi: 10.1093/nargab/lqac007.
Additionally you can cite the pipeline directly with the following doi: 10.5281/zenodo.3589527
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.