oceanomics-amplicon-nf - v1.0.1: Nautilus, improved

What's Changed

• Bugfixes around incomplete sample sheets

Full Changelog: https://github.com/MinderooFoundation/OceanOmics-amplicon-nf/compare/v1.0.0...v1.0.1

- Nextflow
Published by philippbayer about 1 year ago

oceanomics-amplicon-nf - v1.0.0: Nautilus

CHANGELOG - Added Nestering to remove some false positives present mostly in controls - read count filtering based on control samples. See Nester et al. 2024, to quote: 'Instead of entirely removing these ZOTUs, we adjusted the read numbers in each sample, removing the number of reads present in controls or the percentage of the ZOTU comprising the control (whichever was higher). For example, a ZOTU assigned to Clausocalanus brevipes had 21,300 assigned reads of which two (0.009 %) were present in a field control. We therefore removed either two reads or 0.009 % from each sample, whichever resulted in a higher number of reads.'. Which samples are used for Nestering are controlled by the samplesheet column use_for_filter. - Added AquaMaps integration for downstream curation - the pipeline now produces a CSV of Aquamaps probabilities based on species-level sightings to help users find false-positives - Greatly expanded MultiQC report for lab curation and visualisation of results - Greatly expanded output in phyloseq object. Now contains ASVs with no hits at all (filter by NA). - Many, many, many, many bugfixes

Full Changelog: https://github.com/MinderooFoundation/OceanOmics-amplicon-nf/compare/v0.1.0...v1.0

- Nextflow
Published by philippbayer over 1 year ago

oceanomics-amplicon-nf - First release: Thalassa Latest

This is the beta release of Minderoo OceanOmics amplicon pipeline for metabarcoding projects. This release is associated with the article "Exploring the data that explores the oceans: working towards robust eDNA workflows for ocean wildlife monitoring" (DOI: 10.22541/au.169322437.73242445/v1)

Contributors:

@a4000 @philippbayer @Hobbeist @jrpearce

- Nextflow
Published by Hobbeist over 2 years ago