Mapper

cphasing mapper is designed for process Pore-C or CiFi data, its output two files:
(1) porec table (.porec.gz) which contain high-order contacts
(2) 4DN pairs (.pairs.pqs) which only retain VPCs.

Note

The output of CiFi, still named .porec.gz, contains the same results whether Pore-C or CiFi data.

Examples¶

Process one cell Pore-C data¶

cphasing mapper draft.contigs.fasta sample.porec.fastq.gz -t 40

Note

By default, cphasing mapper uses minimap2 as the aligner. You can specify different aligners using the -a or --aligner option: - minimap2 (default): High-performance standard alignment tool. - c3align: More valid contacts for polyploids.

Process multiple cells Pore-C data¶

Process together¶

cphasing mapper draft.contigs.fasta sample1.porec.fastq.gz sample2.porec.fastq.gz -t 40

or

cphasing mapper draft.contigs.fasta sample*.porec.fastq.gz -t 40

Note

It will output results using the sample1.porec as the prefix

Submit each cell to the cluster¶

use multiple scripts to run mapper for each sample

run_sample1.sh

cphasing mapper draft.contigs.fasta sample1.porec.fastq.gz -t 40

run_sample2.sh

cphasing mapper draft.contigs.fasta sample2.porec.fastq.gz -t 40

run_sample3.sh

cphasing mapper draft.contigs.fasta sample3.porec.fastq.gz -t 40

merge results

cphasing porec-merge sample1.porec.porec.gz sample2.porec.porec.gz sample3.porec.porec.gz -o sample.merge.porec.gz
cphasing pairs-merge sample1.porec.pairs.pqs sample2.porec.pairs.pqs sample3.porec.pairs.pqs -o sample.merge.pairs.pqs

Process one cell HiFi-C data¶

cphasing mapper draft.contigs.fasta sample.porec.fastq.gz -t 40 --mm2-params "-x map-hifi"

Process multiple cells HiFi-C data¶

All the steps of this same with processing in the Pore-C data, with the parameter of --mm2-params "-x map-hifi".