PacBio CiFi reads

rdeval supports PacBio CiFi data, allowing:

  • in-silico restriction digestion of reads

  • output of all fragment combinations

  • compatibility with FASTA/FASTQ/BAM/CRAM I/O

Two options enable these features:

--cifi-enzyme <string>

Specifies the restriction enzyme motif used for in-silico digestion.

Example:

rdeval --cifi-enzyme DpnII testFiles/cifi_reads.fastq -o cifi_reads.digested.fastq

--cifi-out-combinations

Outputs all possible combinations of digested fragments per read as paired-end (PE) reads.

Example:

rdeval --cifi-enzyme DpnII --cifi-out-combinations testFiles/cifi_reads.fastq -p rdeval_

For each input file, this will generate two PE files following the naming pattern:

  • <prefix>_1.<ext>

  • <prefix>_2.<ext>

Reference

CiFi: Accurate long-read chromosome conformation capture with low-input requirements https://www.biorxiv.org/content/10.1101/2025.01.31.635566v2