Package: sequana-multitax
This is is themultitaxpipeline from theSequanaprojectOverview:Runs taxonomic analysis on a set of samples using sequana_taxonomy (kraken behing the scene)Input:A set of Fastq filesOutput:HTML report for each sample and a summary HTML report for all samples.Status:ProductionCitation:Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI doi:10.21105/joss.00352InstallationIf you already have all requirements, you can install the packages using pip:pip install sequana_multitax --upgradeUsageIn order to use this pipeline, you will need Kraken databases. Please see Kraken pages for help.We will also need a taxonomic databases. In principle this pipeline will download the file in your home, in
/home/user/.config/sequana/taxonomy.dat one for all. Note, that with singularity, this file will be downloaded locally in your working directory for each analysis,except if it is found in your home, in which case a simple copy is performed.sequana_multitax --help
sequana_multitax --input-directory DATAPATH  --databases toydbFor the database, you will need to provide your own databases. You can check out
the documentation of kraken. The toydb here above is shipped with sequana and
should work for demo. See sequana_taxonomy standalone for more help and
information. You can also checkout the sequana documentation (kraken module).The Kraken final report and blast analysis (if set) will need a taxonomic file
stored in the sequana config directory (HOME/.config/sequana/taxonomy.dat). If
not already done, type this command:sequana_multitax --update-taxonomyYou may need to call this command from time to time if unknown taxon appears in
the HTML reports.This creates a directory with the pipeline and configuration file. You will then need
to execute the pipeline:cd multitax
sh multitax.sh  # for a local runThis launch a snakemake pipeline. If you are familiar with snakemake, you can
retrieve the pipeline itself and its configuration files and then execute the pipeline yourself with specific parameters:snakemake -s multitax.rules -c config.yaml --cores 4 --stats stats.txtOr usesequanixinterface.Usage with singularity::With singularity, initiate the working directory as follows:sequana_multitax --use-singularity ...Images are downloaded in the working directory but you can store then in a directory globally (e.g.):sequana_multitax --use-singularity --singularity-prefix ~/.sequana/apptainersand then:cd multitax
sh multitax.shif you decide to use snakemake manually, do not forget to add singularity options:snakemake -s multitax.rules -c config.yaml --cores 4 --stats stats.txt --use-singularity --singularity-prefix ~/.sequana/apptainers --singularity-args "-B /home:/home"RequirementsThis pipelines requires the following executable(s):kraken2sequana_taxonomykronaYou can download databases from kraken website. We provide some databases onhttps://github.com/sequana/resources. You can download a toy database as follows:sequana_taxonomy --download toydbThe first time, a taxonomic database will be downloaded and stored locally in
.config/sequana/taxonomy.dat file. You can update it from time to time using:sequana_taxonomy --update-taxonomyDetailsThis pipeline runssequana_taxonomy(based on kraken) in parallel on the input fastq files (paired or not).
A brief sequana summary report is also produced. For each sample, a HTML page is
reported with the following kind of image. This pie chart is a static image
summarizing the species found in your sample. Unclassified reads are in grey.
Colors correspond to a kingdom (green for viruses). If you click on the image,
you will be redirect to a more precise pie chart base on Krona pie chart, which
is more interactive.The analysis is enterily based on Kraken tool. If several databases are
provided, they are run sequentially. This requires a careful interpretation of
the results. Indeed analysing data with viruses then bacteria may give different
results as compare to analysing with bacteria then viruses.Rules and configuration detailsHere is thelatest documented configuration fileto be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file.ChangelogVersionDescription0.12.0Refactor to use new Click framework0.11.1add missing import in the main scriptadd wrapper version in config0.11.0use latest wrappers and graphivz apptainercreate and use a sequana-wrappers for the sequana_taxonomy rukefix type when downloading taxonomy.dat0.10.2add singularity containers0.10.1fix blast run when no taxid is found and HTML report0.10.0uses new sequana wrappers and frameworkadd ability to run blast on unclassified readshandle case of empty FastQ files0.9.2add –update-taxonomy DB optionadd –store-unclassified option0.9.1fix a logger issue0.9.0fix plot summary dbs (sample names). Add options in schema+config
file to tune the image if required.HTML now includes links towards data that generates the top plotsfix case where zero sequences are foundcheck existence of input databasesadd the –run argumentadd multitax version in the headeradd search box (Sequana feature) in the CSV tables0.8.7Update HTML report: fix the title of images. include table with DB
proportion. Text to explain images and reports0.8.6A better report with new features from sequana.taxonomy0.8.5fix typo in doc, factorise multiqc rule0.8.4implement the –from-project option0.8.3add the confidence option in sequana_taxonomy ruleimprove html reportuses new sequana framework to speed up –help calls0.8.2less stringent on requirements (mode warning)fix input of the multiqc rule0.8.1Fix requirements.0.8.0First release.