This script aims to find the haplotype-specific duplications that caused by heterozygous variations. Since it is invetible that certain homologous loci exist divergence for most diploid organisms, assemblers might report the same regions twice, one of which is duplicated sequences for a haploid assembly. This script will identify such regions and keep only one sequence of every homologous pair, then integrate it into primary seqeunces, so the other is alternate sequences for corresponding region. In addition, primary sequences also include those consensuses (homozygous regions collapse sequnces from pairf chromosomes).
sh ./hapdup_finder.sh -h
This script identifies haplotype-specific duplications caused by heterozygous variantions.
The names of duplicated sequences will be indicated in the end. The script can be applied
both at the contig and scaffold level
Syntax: sh ./main.sh -f <FA> [-n|x|t|o]
options:
-s Specify when sequence file is scaffolds.
-f FILE Sequence file that is required to inspect haplotype-specific duplicates.
-n INT Number of chromosome-level scaffolds. Only used when -s is activated.
-x FLOAT Upper bound of sequence divergence used in minimap2 alignments.
Allowed input: 0.05, 0.1 (by default) and 0.2. Default: 0.1.
-t INT Number of threads used in minimap2. Default: 3.
-o DIR Output directory. All generated files are put in this directory.
Default: present working directory.
-h Print this help and exit.
minimap2
python 2.7+
samtools (not required if index of sequences, i.e., .fai file, exists)
If -s is activated, which means the input file is at scaffold level ('N' in the sequences), you will get two files naming:
- primary_seqs.fa
- alternate_seqs.fa
If not, i.e., input sequeces are contigs, then you will have two files naming:
- primary_contigs.fa
- alternate_contigs.fa