cifi 0.2.1

CiFi - toolkit for downstream processing of CiFi long reads.

CiFi

Toolkit for downstream processing of CiFi long reads.

https://dennislab.org/cifi

Install

pip install cifi
# or
mamba install bioconda::cifi

Commands

Command	Description
cifi qc	Sample reads and report enzyme site frequency, fragment sizes, estimated yield
cifi digest	In-silico digestion → paired-end FASTQ (all pairwise contacts)
cifi filter	MAPQ-based filtering of aligned paired-end BAM
cifi enzymes	List built-in restriction enzymes

qc

cifi qc reads.bam -e HindIII -o qc_out
cifi qc reads.bam -e NlaIII -n 50000 -o qc_out    # sample 50k reads
cifi qc reads.bam -e HindIII -n 0 -o qc_out        # all reads
cifi qc reads.bam --site GANTC --cut-pos 1 -o qc_out  # custom site

Writes an output directory with HTML report, JSON, TSV tables, distribution plots (PNG), and a multi-page PDF.

digest

cifi digest reads.bam -e HindIII -o output
cifi digest reads.fq.gz -e NlaIII -o output -m 5 --gzip
cifi digest reads.bam --site GANTC --cut-pos 1 -o output

Produces {prefix}_R1.fastq and {prefix}_R2.fastq (optionally gzipped), plus an HTML report and JSON stats.

filter

cifi filter aligned.bam -o filtered.bam -q 30

Keeps properly paired reads where both mates meet the MAPQ threshold.

Enzymes

Built-in enzymes:

4-cutters	6-cutters
NlaIII (CATG)	HindIII (AAGCTT)
DpnII (GATC)
MboI (GATC)
Sau3AI (GATC)

Any recognition site can be specified with --site and --cut-pos, including IUPAC degenerate bases (N, R, Y, W, S, M, K, B, D, H, V).

How it works

CiFi reads are concatemers of restriction fragments from genomic regions in 3D proximity. The toolkit finds all enzyme cut sites in each read, extracts fragments, and generates every pairwise combination as a pseudo paired-end read:

Read with 4 fragments: [A]-[B]-[C]-[D]
Pairs: A-B, A-C, A-D, B-C, B-D, C-D  (6 pairs)

Citation

Coming soon.