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