chr3d digest


chr3d digest [OPTIONS] FASTA

Generate restriction fragment BED from a genome FASTA.

In silico digest a genome FASTA with a restriction enzyme and output a BED file of fragments. This BED file can be passed to bulk-hic / sn-hic via --fragment-bed to enable fragment-aware pair parsing with pairtools.

Examples

Single Enzyme


chr3d digest -e MboI -o hg38_MboI.bed /data/genomes/hg38.fa

Dual Enzyme (Arima Kit)


chr3d digest -e MboI -e GATC^ -o arima_frags.bed /data/genomes/hg38.fa

Custom Recognition Site


chr3d digest -e A^AGCTT -o fragments.bed /data/genomes/hg38.fa

With Size Filtering


chr3d digest -e HindIII --min-size 50 --max-size 500000 -o fragments.bed genome.fa

Supported Enzymes

Enzyme	Recognition Site
`HindIII`	`A^AGCTT`
`DpnII`	`^GATC`
`MboI`	`^GATC`
`BglII`	`A^GATCT`
`Sau3AI`	`^GATC`
`Hinf1`	`G^ANTC`
`NlaIII`	`CATG^`
`AluI`	`AG^CT`
`EcoRI`	`G^AATTC`
`BamHI`	`G^GATCC`
`PstI`	`CTGCA^G`
`SalI`	`G^TCGAC`
`XbaI`	`T^CTAGA`

Or pass the raw recognition site with cut position, e.g., A^AGCTT.

Arguments

Argument	Default	Description
`FASTA`	—	Genome FASTA file (plain or gzipped)
`-e, --enzyme NAME_OR_SITE`	—	Enzyme name or recognition site. Repeat flag for multiple enzymes (Arima kit)
`-o, --output BED`	—	Output BED file path
`--min-size INT`	`20`	Minimum fragment size to keep (bp)
`--max-size INT`	`10000000`	Maximum fragment size to keep (bp)
`-v, --verbose`	—	Enable DEBUG-level logging
`--log-file FILE`	—	Write log to FILE