HAT-phasing 0.0.4

HAT:‌ Haplotype assembly tool that use both long and short reads to reconstruct haplotypes

HAT: Haplotype Assembly Tool

HAT is a haplotype assembly tool that use NGS and TGS data along a reference genome to reconstruct haplotypes. HAT gets a VCF file containing SNPs, sorted bam file of NGS data alignment to the reference, and sorted bam file of TGS data alignment to the reference as input.

Installation

python setup.py install

Requirements

• Python
• pysam
• Biopython
• numpy
• matplotlib
• seaborn

Options

usage: HAT [-h] [-rl READ_LENGTH] [-pl PHASING_LOCATION] [-r REFERENCE_FILE] [-lf LONGREADS_FASTA]
           [-th TRUE_HAPLOTYPES] [-ma MULTIPLE_GENOME_ALIGNMENT] [-ha HAPLOTYPE_ASSEMBLY]
           chromosome_name vcf_file short_read_alignment long_read_alignment ploidy output output_dir

positional arguments:
  chromosome_name       The chromosome which is getting phased
  vcf_file              VCF file name
  short_read_alignment  short reads alignment file
  long_read_alignment   long reads alignment file
  ploidy                ploidy of the chromosome
  output                output prefix file name
  output_dir            output directory

optional arguments:
  -h, --help            show this help message and exit
  -rl READ_LENGTH, --read_length READ_LENGTH
                        short reads length
  -pl PHASING_LOCATION, --phasing_location PHASING_LOCATION
                        the location in the chromosome which is phased
  -r REFERENCE_FILE, --reference_file REFERENCE_FILE
                        reference file
  -lf LONGREADS_FASTA, --longreads_fasta LONGREADS_FASTA
                        long reads fasta file
  -th TRUE_HAPLOTYPES, --true_haplotypes TRUE_HAPLOTYPES
                        the correct haplotypes file
  -ma MULTIPLE_GENOME_ALIGNMENT, --multiple_genome_alignment MULTIPLE_GENOME_ALIGNMENT
                        Multiple genome alignment file of haplotypes to the reference
  -ha HAPLOTYPE_ASSEMBLY, --haplotype_assembly HAPLOTYPE_ASSEMBLY
                        Assembly of the haplotype sequences

Example