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We will update the system on Monday May 17th, 2021. No new jobs will start from the Friday before until the new version is deployed. Please plan accordingly.

Recommended Workflows

Click on the spheres to get more information

Application: Metatranscriptomic
Adapter & host removal, Ribosomal RNA filtering, and Woltka profiling


This workflow will (1) trim autodetected adapter sequences, (2) filter reads mapping to a selected host genome, (3) filter reads mapping to rRNA genes, and (4) run Woltka on the processed reads to generate per-genome and per-gene feature-tables at various taxonomic levels.

This workflow relies on fastp, minimap2, sortmerna and Woltka; more details.

Note that the current recommendation is to run Woltka with the two available databases: Rep200 and WoL as they give different perspectives from the same data. Additionally, this workflow starts from the rawest data available.

Application: 16S, 18S
Trimming and Deblur and/or Closed Reference OTU-picking


This workflow will (1) trim your reads to a selected read length, and (2) run either Deblur or closed-reference-picking to generate a feature-table.

Note it starts on a demultiplexed artifact; which means that the raw data needs to be demultiplexed and/or QC-ed. More details.

Extra: The Deblur command actually includes a fragment insertion step via SEPP.

Application: Metagenomic
Adaptor & host removal, and Woltka profiling


This workflow will (1) trim autodetected adapter sequences, (2) filter reads mapping to a selected host genome, and (3) run Woltka on the processed reads to generate per-genome and per-gene feature-tables at various taxonomic levels.

This workflow relies on fastp, minimap2, and Woltka. More info

Note that the current recommendation is to run Woltka with the two available databases: Rep200 and WoL as they give different perspectives from the same data. Additionally, this workflow starts from the rawest data available.