MODULES.md

Modules

leviathan-preprocess

Preprocesses data into form than can be used by leviathan-index

leviathan-preprocess.py \
    -i references/manifest.tsv \
    -a references/pykofamsearch.pathways.tsv.gz \
    -o references/

leviathan-index

Build, update, and validate leviathan database

leviathan-index.py \
    -f references/cds.fasta.gz \
    -m references/feature_mapping.tsv.gz \
    -g references/genomes.tsv.gz \
    -d references/index/ \
    -p=-1

leviathan-info

Report information about leviathan database

leviathan-info.py -d references/index/

leviathan-profile-taxonomy

Profile taxonomy using Sylph with leviathan database

leviathan-profile-taxonomy.py \
    -1 fastq/example_1.fastq.gz \
    -2 fastq/example_2.fastq.gz \
    -n example \
    -d references/index/ \
    -o leviathan_output/profiling/taxonomy/ \
    -p=-1

leviathan-profile-pathway

Profile pathways using Salmon with leviathan database

leviathan-profile-pathway.py \
    -1 fastq/example_1.fastq.gz \
    -2 fastq/example_2.fastq.gz \
    -n example \
    -d references/index/ \
    -o leviathan_output/profiling/pathway/ \
    -p=-1

leviathan-merge

Merge sample-specific taxonomic and/or pathway profiling

leviathan-merge.py \
    -t leviathan_output/profiling/taxonomy/ \
    -p leviathan_output/profiling/pathway/ \