An ultra-fast and accurate tool for de novo assembly of organelle genome from whole genome data
usage: panplasty -1 PE1.fq.gz -2 PE2.fq.gz -x pc -s 6421 -o plant_cp
An ultra-fast and accurate tool for de novo assembly of organelle genome from whole genome data
Input/Output options:
-1 , --fx_1 paired-end fasta/q file1
-2 , --fx_2 paired-end fasta/q file2
-r , --fx_r single-end fasta/q file
-s , --name sample name
-o , --out output directory
-x , --tax organelle type to assemble:
Animals mitochondrial (am)
Fungi mitochondrial (fm)
Plants chloroplast (pc)
Plants mitochondrial (pm)
Reads filter options:
-u , --unknown max ratio of unknown (N) base [0.15]
-a , --min_qual min average base quality for fastq reads [20]
-e , --hfk_kmer hfk kmer size [31]
-w , --hfk_win hfk window size [5]
-q , --hfk_freq min kmer frequency for high freq kmer [3]
-c , --hfk_count min count of read with high freq kmer [auto]
Assembly options:
-k , --k_min min kmer size for assembly [auto]
-f , --k_freq min kmer frequency for assembly [5]
-m , --k_max max kmer size for assembly [auto]
-p , --k_step increment of kmer size for assembly [10]
-d , --d_min min kmer depth of organelle contig [15]
-l , --map_len min read mapping length for local assembly [auto]
-i , --read_iden min read mapping identify for local assembly [0.95]
Polishing options:
-Q , --map_quality min mapping quality [1]
-D , --var_depth min reads number that support a variation [5]
-V , --var_ratio min ratio of variation reads to total depth [0.6]
Other options:
-n , --reads_number min number of reads to be used for round 1 assembly [auto]
-R , --max_rounds max number of extending rounds for assembly [10]
-t , --threads number of threads [1]
-h, --help show this help message and exit
--version print version