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Co-authored-by: Daniel Lundin <matricaria.suaveolens@gmail.com>
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d4straub and erikrikarddaniel committed Jul 26, 2024
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2 changes: 1 addition & 1 deletion CHANGELOG.md
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Expand Up @@ -8,7 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### `Added`

- [#765](https://github.com/nf-core/ampliseq/pull/765) - Added version R09-RS220 of curated GTDB 16S taxonomy: `sbdi-gtdb=R09-RS220-1` or `sbdi-gtdb` as parameter to `--dada_ref_taxonomy`
- [#766](https://github.com/nf-core/ampliseq/pull/766) - Added version 10 of Unite as options for `--sintax_ref_taxonomy`
- [#766](https://github.com/nf-core/ampliseq/pull/766) - Added version 10 of Unite as parameter for `--sintax_ref_taxonomy`: `unite-fungi=10.0` and `unite-alleuk=10.0`

### `Changed`

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2 changes: 1 addition & 1 deletion conf/test_its_dada_taxonomy.config
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params {
config_profile_name = 'Test sintax profile'
config_profile_description = 'Minimal test dataset to check pipeline function when using sintax for taxonomy assignment'
config_profile_description = 'Minimal test dataset to check pipeline function for ITS data with the DADA2 taxonomy classifier'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
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2 changes: 1 addition & 1 deletion docs/output.md
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Expand Up @@ -202,7 +202,7 @@ Optionally, ASV sequences can be filtered for rRNA sequences identified by Barrn

#### Length filter

Optionally, a length filter can be used to reduce potential contamination after ASV computation. For example with 515f and 806r primers the majority of 16S rRNA amplicon sequences should have a length of 253 bp and amplicons that vary significantly are likely spurious.
Optionally, a length filter can be used to reduce potential contamination after ASV computation. For example with 515f and 806r primers the majority of 16S rRNA amplicon sequences should have a length of 253 bp and amplicons that differ significantly from this are likely spurious.

The minimum ASV length threshold can be set by `--min_len_asv` and the maximum length threshold with `--max_len_asv`. If no threshold is set, the filter (and output) is omitted.

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