Gears is a metagenomics pipeline. (``GE``nome ``A``nnotation of ``R``esidual ``S``equences). One can use this pipeline to identify contamination in sequencing runs on either raw FastQ files or BAM files.
In case of BAM file as input, it will extract the unaligned read(pair) sequences for analysis.
Analysis result is reported in a sunburst graph, which is visible and navigatable in a webbrowser.
| -sample | --sampleid | String (**required**) | Name of sample |
| -library | --libid | String (**required**) | Name of library |
If `-R2` is given, the pipeline will assume a paired-end setup. `-bam` is mutualy exclusive with the `-R1` and `-R2` flags. Either specify `-bam` or `-R1` and/or `-R2`.
### Config
## Result files
The results of `Gears` are stored in the following files:
| *.krkn.full | kraken-report | tsv | List of all annotation possible with counts filled in for this specific sample|
| *.krkn.json | krakenreport2json| json | JSON representation of the taxonomy report, for postprocessing |
In a seperate `report` folder, one can find the html report displaying the summary and providing a navigation view on the taxonomy graph and (its) result.
## Getting Help
For questions about this pipeline and suggestions, we have a GitHub page where you can submit your ideas and thoughts .[GitHub](https://github.com/biopet/biopet).
Or contact us directly via: [SASC email](mailto:SASC@lumc.nl)