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The development of this workflow was supported by NFDI4Microbiota 
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SameStr is a tool for strain-level analysis and microbial tracking with genomic/metagenomic data originally developed in the Fricke Lab at the University of Hohenheim. The SameStr workflow is a nextflow workflow for running SameStr based on MetaPhlAn4 marker alignments, including optional read preprocessing and host/human decontamination steps provided by the nevermore workflow library.
This workflow:
Also cite:
Podlesny D, Arze C, Dörner E, et al. Metagenomic strain detection with SameStr: identification of a persisting core gut microbiota transferable by fecal transplantation. Microbiome. 2022;10(1):53. Published 2022 Mar 25. doi:10.1186/s40168-022-01251-w
The easiest way to handle dependencies is via Singularity/Docker containers. Alternatively, conda environments, software module systems or native installations can be used.
Preprocessing and QA is done with bbmap, fastqc, and multiqc.
Decontamination is done with kraken2 and additionally requires seqtk.
Host removal requires a kraken2 host database.
The default supported MetaPhlAn version is 4.
Get an SGB-based CHOCOPhlAn database from the official Biobakery site. At the time of writing, the following databases are available:
mpa_vJan21_CHOCOPhlAnSGB_202103(has SameStr db)mpa_vOct22_CHOCOPhlAnSGB_202212(has SameStr db)mpa_vJun23_CHOCOPhlAnSGB_202307(has SameStr db)mpa_vOct22_CHOCOPhlAnSGB_202403(not tested)mpa_vJun23_CHOCOPhlAnSGB_202403(not tested)
To install the database, unpack the tarball and point the --mp4_db parameter to the database's root directory.
In params.yml:
mp4_db: "/path/to/mpa_vOct22_CHOCOPhlAnSGB_202212/"
On the command line:
--mp4_db "/path/to/mpa_vOct22_CHOCOPhlAnSGB_202212/"
Shared strains are detected with SameStr.
Obtain the SameStr database corresponding to your CHOCOPhlAn database from the Zenodo repository.
This workflow will be available on the CloWM platform (coming soon).
The workflow run is controlled by environment-specific parameters (see run.config) and study-specific parameters (see params.yml). The parameters in the params.yml can be specified on the command line as well.
You can either clone this repository from GitHub and run it as follows
git clone https://github.com/grp-bork/samestr_flow.git
nextflow run /path/to/samestr_flow [-resume] -c /path/to/run.config -params-file /path/to/params.yml
Or, you can have nextflow pull it from github and run it from the $HOME/.nextflow directory.
nextflow run grp-bork/samestr_flow [-resume] -c /path/to/run.config -params-file /path/to/params.yml
Fastq files are supported and can be either uncompressed (but shouldn't be!) or compressed with gzip or bzip2. Sample data must be arranged in one directory per sample.
All files in a sample directory will be associated with the name of the sample folder. Paired-end mate files need to have matching prefixes. Mates 1 and 2 can be specified with suffixes _[12], _R[12], .[12], .R[12]. Lane IDs or other read id modifiers have to precede the mate identifier. Files with names not containing either of those patterns will be assigned to be single-ended. Samples consisting of both single and paired end files are assumed to be paired end with all single end files being orphans (quality control survivors).