pstools: Toolkit for fully phased sequences on chromosome level

Routine production of phased sequences (haplotypes) of genomes are important to study variation occurring in complex cancer and healthy samples. We developed a novel graph-based algorithm to integrate HiFi and Hi-C data types to produce haplotypes at the base-level resolution for routine clinical research. When benchmarking our method on healthy human genomes, we produced significantly high-quality genomes with a sequence continuity NG50 >130 Mb, switch/hamming error rates <1.5% and a completeness of >6.0 Gb, and an order of magnitude faster process (only <12 hours). This simple approach will facilitate improvement in understanding of the mechanisms of clinical diseases.

Installation

(requiring g++ and zlib)
git clone https://github.com/shilpagarg/pstools.git
cd pstools && make

Execution

Once you compiled the repo, you will see binary file pstools in the same directory. Now you are ready to go to produce fully phased sequences on chromosome level.

# Use Hi-C data and node sequences of hifiasm graph (awk '/^S/{print ">"$2;print $3}' hifiasm_r_utg.gfa > hifiasm_r_utg.fa)
pstools hic_mapping -t32 -o <map.out> <hifiasm_r_utg.fa> <hic.R1.fastq.gz> <hic.R2.fastq.gz>

# Use Hi-C mapped reads through hifiasm graph to produce fully phased sequences
pstools resolve_haplotypes -t32 -i true <map.out> <hifiasm_r_utg.gfa> <out>
# where `map.out` is the file from above process, `hifiasm_r_utg.gfa` is the hifiasm r_utg graph and `out` is the output directory name.
This command produces fully phased sequences in `pred_hap1.fa` and `pred_hap2.fa`.  

Results

Table shows the benchmarking results of HG002 using OmniC or Arima genomics data:

|<sub>Hi-C dataset<sub>|<sub>Size<sub>|<sub>CPU time<sub>|<sub> NG50<sub>|<sub> QV<sub>| |:---------------|-----:|--------------------:|:----------|-------:| |_[HG002]|_~6.1Gb |_~5h |_{~132 Mb}|_~Q50|

For further experiments, please run `experiments.sh`.

Limitations

1. At the current stage, the phased sequences don't contain centromeric regions.
2. The UL nanopore data is not used.
3. Need to be tested on trio-hifiasm graph

Note that pstools is under active development. For any issues or suggestions, please create an issue or a pull request.