##Detect two haplotypes in genome assembly using reference genome
This program aims to identify two haplotype sequences within a genome assembly guided by a reference genome. A common problem in genome assembly of heterozygous genome using Illumina short reads is two haploid genome were assembled separately. The detection of these sequences is very important and interesting to some biologists, e.g. studying the origins, mutations and structural variations between the two haploid genomes especially from a hybrid species and investigating X-linked and Y-linked genes etc.
####Workflow:
- Extract exon sequences from the reference genome
- Identify scaffolds of heterozygous genome which contain exons from a reference genome using blastn
- blast-2-sequences the top 2 best hit for each exon
- Identify syntenic blocks using DAGchainer
##Getting started
####Install the following dependencies:
- Executable for blastn
- Executable for makeblastdb
- Executable for dagchainer
*Note: Full path must be specified in the script if the executable is not found in the path
####Usage
usage: find2genomehaplo.py [-h] infile ref gff
Identify two haplotypes in a higly heterozygous genome assembly using
reference genome
positional arguments:
infile fasta file of heterozygous genome
ref fasta file of masked reference genome
gff gff3 file of reference genome
optional arguments:
-h, --help show this help message and exit####Output files
- The file "dagchainer.dat.aligncoords" contains the results for the two identified haplotypes. Filtering is required to summarize the results.
- This pipeline keeps a number of temporary files which make it easier to re-run if the process is interrupted (exon.fa, allexon.blast, unique_pair.dat, top2_blast.tagset, b2seq.blast, dagchainer.dat)