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Sofia Stamouli 2022-10-11 17:29:41 +02:00
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@ -200,7 +200,7 @@ Complexity filtering is primarily a run-time optimisation step. It is not necess
There are currently three options for short-read complexity filtering: [`bbduk`](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/), [`prinseq++`](https://github.com/Adrian-Cantu/PRINSEQ-plus-plus), and [`fastp`](https://github.com/OpenGene/fastp#low-complexity-filter).
There is one option for long-read quality filtering: [`Filtlong`](https://github.com/rrwick/Filtlong)
There is one option for long-read quality filtering: [`Filtlong`](https://github.com/rrwick/Filtlong)
The tools offer different algorithms and parameters for removing low complexity reads and quality filtering. We therefore recommend reviewing the pipeline's [parameter documentation](https://nf-co.re/taxprofiler/parameters) and the documentation of the tools (see links above) to decide on optimal methods and parameters for your dataset.