Examples of reports generated with GRIMER
original publication: 10.1186/s40168-018-0575-4
# Download files (table, metadata and config) wget https://raw.githubusercontent.com/pirovc/grimer-reports/main/placenta/placenta_files.tar.gz tar xf placenta_files.tar.gz # Run GRIMER # AMPLICON grimer --config placenta_amplicon_config.yaml \ --input-file placenta_amplicon_table.tsv \ --metadata-file placenta_metadata.tsv \ --taxonomy ncbi \ --ranks superkingdom phylum class order family genus species \ --level-separator ";" \ --obs-replace "^.+__" "" "_" " " \ --unassigned-header "Unassigned" \ --decontam --mgnify --transpose \ --title "Placenta study AMPLICON - Leiby, J.S. et al 2018" \ --output-html placenta_amplicon.html # MGS grimer --config placenta_mgs_config.yaml \ --input-file placenta_mgs_table.tsv \ --metadata-file placenta_metadata.tsv \ --taxonomy ncbi \ --ranks superkingdom phylum class order family genus species \ --level-separator "|" \ --unassigned-header "unassigned" \ --decontam --mgnify \ --title "Placenta study MGS - Leiby, J.S. et al 2018" \ --output-html placenta_mgs.html
original publication: 10.1128/mSystems.00218-17
# Download files (table, metadata and config) wget https://raw.githubusercontent.com/pirovc/grimer-reports/main/katharoseq/katharoseq_files.tar.gz tar xf katharoseq_files.tar.gz # Run GRIMER grimer --config katharoseq_config.yaml \ --input-file katharoseq_table.tsv \ --metadata-file katharoseq_metadata.tsv \ --transformation clr \ --obs-replace "^.+__" "" "_" " " \ --taxonomy ncbi \ --ranks superkingdom phylum class order family genus species \ --level-separator ";" \ --decontam --mgnify \ --title "KatharoSeq - Minich et al. 2018" \ --output-html katharoseq.html
original publication: 10.1038/nmicrobiol.2016.24
# Download files (table, metadata and config) - Original source: https://microbiomedb.org/common/downloads/release-22/82fe0308e2032de2041694df6592ba542ea84b86/ResistomeAmplicon.16s_DADA2.taxon_abundance.biom wget https://raw.githubusercontent.com/pirovc/grimer-reports/main/microbiomedb/microbiomedb_files.tar.gz tar xf microbiomedb_files.tar.gz # Run GRIMER grimer --config ResistomeAmplicon.16s_DADA2_config.yaml \ --input-file ResistomeAmplicon.16s_DADA2.taxon_abundance.biom \ --taxonomy ncbi \ --ranks superkingdom phylum class order family genus species \ --decontam --mgnify \ --title "MicrobiomeDB Preterm Infant Resistome (V4)" \ --output-html ResistomeAmplicon.html
original publication 10.7554/elife.35987
# Script to download files and generate GRIMER report from any MGnify study accession # Requires "jsonapi-client>=0.9.7" (conda install "jsonapi-client>=0.9.7") ./grimer-mgnify.py -i MGYS00005180 -o MGYS00005180 -g "--decontam --mgnify" # Or directly from files wget https://raw.githubusercontent.com/pirovc/grimer-reports/main/mgnify/mgnify_files.tar.gz tar xf mgnify_files.tar.gz # Run GRIMER grimer --config MGYS00005180_config.yaml \ --input-file MGYS00005180_ERP108433_taxonomy_abundances_SSU_v4.1.tsv \ --metadata-file MGYS00005180_metadata.tsv \ --obs-replace "^.+__" "" "_" " " \ --taxonomy ncbi \ --ranks superkingdom kingdom phylum class order family genus species \ --level-separator ";" \ --decontam --mgnify \ --title "MGnify study accession MGYS00005180" \ --output-html MGYS00005180.html