ampliseq
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nf-core
Amplicon sequencing analysis workflow using DADA2 and QIIME2
### Description of feature @johnne is working on making a version of the CO1 database better adapted to the GBIF backbone taxonomy. When that is available, make sure it's selectable...
### Description of feature The SINTAX algorithm by Robert Edgar is apparently better for certain taxa/databases, primarily by being more strict and not providing so many false positives. Add as...
@erikrikarddaniel, I have made a few changes in the ASV database that may require adaptation of ampliseq output: 1) _materialSampleID_ should, if supplied, be a _link to_ an archived sample,...
Version `2.5` of [nf-core/tools](https://github.com/nf-core/tools) has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline. Please make sure to...
This updates QIIME2 to the most recent container, Picrust2, and nf-core modules. Hm, tests worked locally, but in CI they fail with: ``` Error executing process > 'NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_EXTRACT (GTGYCAGCMGCCGCGGTAA-GGACTACNVGGGTWTCTAAT)' Caused...
### Description of feature As mentioned in [#449](https://github.com/nf-core/ampliseq/issues/449), filtering out ASVs with stops in translation can make a small but very accurate impact on ensuring correct ASVs. Adding this to...
### Description of the bug I have download the ampliseq pipeline singularity as follow: nf-core download then I run nextflow run nf-core/ampliseq -profile test,singularity --outdir test but it fails with:...
### Description of feature This relates to https://github.com/nf-core/ampliseq/issues/368#issuecomment-1041150714 Essentially, it would be nice to use the provided metadata to make relative abundance means across groups and probably immediately barplots with...
Hi, A very helpful feature to add would be the demultiplexing of the reads as an optional step. This [function](https://docs.qiime2.org/2018.11/plugins/available/demux/) has already been developed on QIIME2 and, as such, it...
## Is your feature request related to a problem? Please describe PhytoRef is a 16S database of chloroplast sequences: http://phytoref.sb-roscoff.fr/ ## Describe the solution you'd like Add the database to...