Alleles
Alleles aims to identify the allelic contig pairs by pairwise comparison.
cphasing alleles -h
Usage: cphasing alleles [OPTIONS]
Build allele table by kmer similarity.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ * --fasta -f polyploid contig-level fasta. │
│ (FILE) │
│ [required] │
│ --output -o path of output allele table [default: │
│ fasta_prefix.allele.table] │
│ (PATH) │
│ -k kmer size for similarity calculation. │
│ (INT) │
│ [default: 19] │
│ -w minimizer window size for similarity calculation. │
│ (INT) │
│ [default: 19] │
│ -c max occurance of allelic pairs │
│ (INT) │
│ [default: 60] │
│ -n minimum chain end │
│ (INT) │
│ [default: 5] │
│ -m minimum k-mer similarity for similarity calculation. │
│ (FLOAT) │
│ [default: 0.5; 0<=x<=1] │
│ -d minimum different threshold between contig pairs. │
│ (FLOAT RANGE) │
│ [default: 0.1; 0<=x<=1] │
│ --threads -t Number of threads. │
│ (INT) │
│ [default: 4] │
│ --help -h,-help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
Examples#
Total length of genome < 10 Gb#
Total length of genome >= 10 Gb#
Warning
Now, alleles do not support contig with a length larger than 135 Mb.