Prepartition¶

The prepartition command is designed to pre-cluster contigs by mapping them to a closely related reference genome.

When a high-quality reference genome of a closely related species (or a monoploid reference) is available, this step provides a reliable initial grouping of contigs based on synteny. This pre-partitioned result can then be passed to the main CPhasing pipeline to guide and accelerate the clustering process.

Basic Usage¶

Run prepartition by providing the reference genome and your draft contigs:

cphasing prepartition monoploid.fasta contigs.fasta -t 40 -o prepartition.clusters.txt

Integration with CPhasing Pipeline¶

Once the prepartition.clusters.txt file is generated, you can use it in the main cphasing pipeline by specifying the -fc (first cluster) parameter. This allows the pipeline to skip the initial clustering and directly use the reference-guided groups for subsequent phasing.

cphasing pipeline -f contigs.fasta \
                  -hic1 hic_R1.fastq.gz \
                  -hic2 hic_R2.fastq.gz \
                  -t 40 \
                  -n 12:4 \
                  -hcr \
                  -p GATC \
                  -fc prepartition.clusters.txt