GRIMER

Examples of reports generated with GRIMER

Data analysis from Leiby et al. "Lack of detection of a human placenta microbiome in samples from preterm and term deliveries"

original publication: 10.1186/s40168-018-0575-4

GRIMER report MGS

GRIMER report AMPLICON

commands used to create report 
# 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

KatharoSeq analysis from Minich et al. "KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples"

original publication: 10.1128/mSystems.00218-17

GRIMER report

commands used to create report 
# 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

Preterm Infant Resistome downloaded from MicrobiomeDB

original publication: 10.1038/nmicrobiol.2016.24

GRIMER report

commands used to create report 
# 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

Antibiotic induced changes in the microbiota disrupt redox dynamics in the gut downloaded from MGnify

original publication 10.7554/elife.35987

GRIMER report

commands used to create report 
# 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