Recommended Workflows

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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.