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SOFTWARE

User-friendly tools, workflows and custom pipelines for microbial multi-omics data analysis

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Metapolish

The merging, annotation & polishing tool for metabolite peak list data

Metapolish is a R tool that allows easy data processing of common Liquid- and Gas Chromatography Mass Spectrometry (LC-/GCMS) raw peak data. The tool bridges the gap between the individual sample peak list outputs generated by MS-analysis software like Thermo Xcalibur-TraceFinder or Shimadzu GCMS solution and the standardised metabolite-concentration matrix input required by downstream metabolite analysis applications such as MetaboAnalyst.

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PuntSeq

A simple, fast, inexpensive and reliable freshwater metagenomics workflow

Clean freshwater lies at the heart of human society. While most traditional water monitoring approaches test for specific chemicals or pathogens, the direct tracing of aquatic DNA poses a more holistic alternative which has hitherto been underappreciated due to challenges in logistics and investment. Here we present a simple, fast, inexpensive and reliable freshwater diagnostics workflow centred around portable nanopore DNA sequencing. 

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NGS pipelines

Custom Snakemake pipelines for reproducible analysis of microbial sequencing data

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Supplementary Data

Llavero-Pasquina et al. (2022)

Here, we provide the supplementary data supporting Llavero-Pasquina et al., "Thiamine metabolism genes in diatoms are not regulated by thiamine despite the presence of predicted riboswitches" published 2022 in New Phytologist. 

Urban & Holzer et al. (2021)

Here, we provide the supplementary data supporting Urban & Holzer et al., "Freshwater monitoring by nanopore sequencing" published 2021 in eLife. Download the raw data from our ENA repository.

Holzer (2019)

Here, we provide the supplementary data supporting Holzer, "The Chlamydomonas reference genomes for visualisation in IGV" published 2019.

Helliwell et al. (2016)

Here, we provide the supplementary data supporting Helliwell et al., "Cyanobacteria and eukaryotic algae use different chemical variants of vitamin B12" published 2016 in Current Biology.

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