Clustering analysis mode

In the clustering mode, the tool RATTLE will be run and the clusters obtained will be further collapsed using CAP3. For RATTLE, use the parameter --rattle_clustering_options '--raw' to use all the reads without any length filtering during the RATTLE clustering step if your amplicon is known to be shorter than 150 bp.

When the amplicon is of known size, we recommend setting up the parameters --lower-length [number] (by default: 150) and --upper-length [number] (by default: 100,000) to filter out reads shorter and longer than the expected size.

Set the parameter --rattle_clustering_options '--rna' and --rattle_polishing_options '--rna' if the data is direct RNA (disables checking both strands).

Example in which all reads will be retained during the clustering step:

nextflow run eresearchqut/ontvisc -resume -profile {singularity, docker} \
                            --analysis_mode clustering \
                            --rattle_clustering_options '--raw' \
                            --blast_threads 8 \
                            --blastn_db /path/to/ncbi_blast_db/nt

Example in which reads are first quality filtered using the tool chopper (only reads with a Phread average quality score above 10 are retained). Then for the clustering step, only reads ranging between 500 and 2000 bp will be retained:

nextflow run eresearchqut/ontvisc -resume -profile {singularity, docker} \
                            --qual_filt --qual_filt_method chopper --chopper_options '-q 10' \
                            --analysis_mode clustering \
                            --rattle_clustering_options '--lower-length 500 --upper-length 2000' \
                            --blast_threads 8 \
                            --blastn_db /path/to/ncbi_blast_db/nt