Invoking sieve

Do you want to reconstruct MAGs from a specific sample?

Only one sample as the input. No filters are applied.

nextflow run . \
    -with-singularity sieve.sif \
    --sample_accession ERS1073737 \
    --cat_db /your/path/to/cat_db --cat_taxonomy /your/path/to/cat_tax \
    --resultsDir output \
    --nodiamond --nomacsyfinder

Do you want to reconstruct MAGs from a specific organism?

Same sample as the input with a taxonomic filter at order level.

nextflow run . \
    --sample_accession ERS1073737 --taxonomyorder legionellales \
    --cat_db /your/path/to/cat_db --cat_taxonomy /your/path/to/cat_tax \
    --resultsDir output \
    --nodiamond --nomacsyfinder

Do you want to reconstruct MAGs by looking for specific genes?

Same sample as input. Same taxonomic filters. New filter: Identification of genes of interest to the user. (All genes must be in fasta format in the same folder. Specify the real path of the folder in the –gene parameter)

nextflow run . \
    --sample_accession ERS1073737 --taxonomyorder legionellales \
    --genes path/to/my/genes/ --diamond_min_align_reads 2 \
    --cat_db /your/path/to/cat_db --cat_taxonomy /your/path/to/cat_tax \
    --resultsDir output \
    --nomacsyfinder

Do you want to reconstruct MAGs by looking for macromolecular system? Pathways?

Same sample as input. Same taxonomic filter. Gene identification filter is also applied. New filter: Identification of macromolecular systems of interest to the user. (You can use a pre-built model from macsydata or your own).

nextflow run . \
    --sample_accession ERS1073737 --taxonomyorder legionellales \
    --genes path/to/my/genes/ --diamond_min_align_reads 2 \
    --model TXSScan --nbmodel bacteria/diderm/T1SS --coverage 0.7 \
    --cat_db /your/path/to/cat_db --cat_taxonomy /your/path/to/cat_tax \
    --resultsDir output

Do you want to reconstruct MAGs using specific binning algorithm and quality criteria?

Same input and filters as above. Only one binning algorithm is used here (concoct). We decide to change the binning size (default 1000). And we want to annotate and classify only bin with a completeness of 70% and a contamination of maximum 20% (i.e. a redundancy of 1.2).

nextflow run . \
    --sample_accession ERS1073737 --taxonomyorder legionellales \
    --genes path/to/my/genes/ --diamond_min_align_reads 2 \
    --model TXSScan --nbmodel bacteria/diderm/T1SS --coverage 0.7 \
    --nomaxbin2 --chunk_size 1200 --completeness 0.7 --redundancy 1.2 \
    --cat_db /your/path/to/cat_db --cat_taxonomy /your/path/to/cat_tax \
    --resultsDir output

Do you want to use local and public metagenomes?

The input will be some local metagenomes (single end) and metagenomes from the aquatic biome. We are looking for gammaproteobacterial genomes that contain specific genes and macromolecular systems. We classify all bins here, even those with less than 50% completeness and more than 10% contamination. We also specify the maximum number of CPUs, memory and time for the HPC cluster (for the base.config file).

nextflow run . \
    --local --local_input path/to/samplesheet.csv --single-end \
    --biome_name water --experiment_type metagenomic --taxonomyclass gammaproteobacteria \
    --genes path/to/my/genes/ --diamond_min_align_reads 2 \
    --model yourmodel --modelpath path/to/your/model --coverage 0.7 \
    --megabinpenalty 0.7 --class_all_bins \
    --cat_db /your/path/to/cat_db --cat_taxonomy /your/path/to/cat_tax \
    --resultsDir output \
    --max_cpus 16 --max_memory 128.GB --max_time 72.h