Home - quadram-institute-bioscience/gmh-sops GitHub Wiki

Welcome to the gmh-sops wiki!

Pipelines

• Human reads removal
• Metagenomes and Metaviromes
  • Metavirome specific pipeline: MetaPhage
• MAGs and Bacterial isolates (MisoFlow)

Galaxy pipelines

Available from QIB Intranet - documented in Confluencs

• QC of shotgun metagenomics (Galaxy)
• Read profiling of shotgun metagenomics (Galaxy)
• Assembly-based analyses of shotgun metagenomics (Galaxy)

Methods

• Metabarcoding analysis using Lotus 1.64
• Metabarcoding analysis using Dadaist2
• Metabarcoding analysis hybrid Qiime2/Dadaist2
• Whole Metagenome Shotgun profiling (2020)
• Whole Metagenome Shotgun functional profiling (2021-2022)

Notes

Tools

• Standard packages
• kraken2
• phylophlan3
• Metaphlan and Humann output files

External pipelines

• nf-core/MAG