Table 1.

Qualitative comparison of the tools for pairs extraction from 3C+ sequencing data.

Tool	Short description	Input	Output	Modular	Flexible	Aligner	Restriction sites	Quality control	Support for modified 3C+ protocols
Pairtools	python API/CLI tools	.sam alignments	pairs	Yes	Yes	bwa mem, bwa mem2, minimap2, bwa aln	Yes	Aggregated stats, scaling	Haplotype-resolved; chemical modification-based; multi-contact; single-cell
Chromap 63	single executable	.fastq reads	contact maps	No	No	chromap	No	No	No
Juicer 64	java/shell script pipeline	.fastq reads	pairs and contact maps	No	Yes	bwa mem	Yes	Aggregated stats	Haplotype-resolved
HiC-Pro 65	python/R/shell script pipeline	.fastq reads	pairs and contact maps	No	Yes	bowtie2	Yes	QC report	Haplotype-resolved
HiCExplorer 66	python API/CLI tools	.sam alignments	contact maps	Yes *	Yes	bwa mem	Yes	QC report	No
FANC 67	python API/CLI tools	.fastq reads or .sam alignments	pairs	Yes	Yes	bwa mem, bowtie2	Yes	QC report	No
TADbit 68	python API/CLI tools	.fastq reads or .sam alignments	parsed reads or contact maps	Yes	Yes	gem, bowtie2, hisat	Yes	Yes	No

We consider methods modular if they have multiple tools that can be used separately or combined in a custom order. HiCExplorer is modular, but its tool for contact extraction is not (indicated with *). We consider methods flexible if they allow parameterization of data processing (e.g., restriction enzyme). We do not consider control only over technical parameters, like the number of cores, to be flexible. For restriction sites, we consider whether a method can either annotate or filter by restriction site.