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Update output.md
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muabnezor authored Nov 22, 2024
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Expand Up @@ -124,7 +124,7 @@ The pipeline uses porecho_abi or porechop to perform adaptertrimming of the long

### Long read filtering

The pipeline uses filtlong, chopper, or nanoq for quality filtering of long reads, specified with `--longread_filtering_tool <filtlong|chopper|nanoq>`. Only is capable of filtering long reads against short reads, and is therefore currently recommended in the hybrid mode. If chopper is selected as long read filtering tool, Lambda Phage removal will be performed with chopper as well, instead of nanolyse.
The pipeline uses filtlong, chopper, or nanoq for quality filtering of long reads, specified with `--longread_filtering_tool <filtlong|chopper|nanoq>`. Only filtlong is capable of filtering long reads against short reads, and is therefore currently recommended in the hybrid mode. If chopper is selected as long read filtering tool, Lambda Phage removal will be performed with chopper as well, instead of nanolyse.

<details markdown="1">
<summary>Output files</summary>
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