3TX_species
Introduction
3TX_species assigns the closest bacterial or viral species to the input reads.
Run Analysis 3TX_species
Once the analysis 3TX_species has been selected from the run analyses interface, the user will be able to select which bioinformatic tool to use. The available tool is:
- kmerfinder - Prediction of bacterial species using a fast K-mer algorithm (assegnazione di specie batteriche)
3TX_species requires input sequences from de novo assembly or mapping; if the latter are provided, the reference genome that has been used for mapping will also be required.
The input selection UI delivers an advanced input selection mode, to allow selection of all types of supported input files at once.
Accepted inputs can be from:
A link to Check analysis will be created after launching the requested analysis. The system will notify the user after a succesful analysis launch and once execution has ended.
Output directory
Please refer to Cohesive's specific Wiki page for information on file download.
The output directory is available at the link in the download page or at the link presente in the analysis' summary card, and will have the following structure: results > YEAR > ID > 3TX_species > DSXXXXXXXX-DTXXXXXX_kmerfinder. The last directory's suffix will be replaced with the name of the chosen tool. At that path there will be 2 directories:
- meta: ("metadata") contains log and configuration files.
- result: contains the analysis' output files.
The table below list files produced by tools available for 3TX_species.
kmerfinder
| File | Description | Location |
|---|---|---|
| DSXXXXXXXX-DTXXXXXX_ID_kmerfinder_bacterial.tsv | file with the assigned batterial species | results directory |
| DSXXXXXXXX-DTXXXXXX_ID_kmerfinder_viral.tsv | file with the assigned viral species | results directory |
