POLAP - Plant organelle DNA long-read assembly pipeline.
version 0.2.4

Usage: polap <menu> [<menu2> [<menu3>]] [-l|--long-reads <arg>] [-o|--outdir <arg>] [-a|--short-read1 <arg>] [-b|--short-read2 <arg>] [--sra <arg>] [-p|--unpolished-fasta <arg>] [-f|--final-assembly <arg>] [-m|--min-read-length <arg>] [-t|--threads <arg>] [-c|--coverage <arg>] [-r|--pair-min <arg>] [-x|--bridge-min <arg>] [-w|--single-min <arg>] [-i|--inum <arg>] [-j|--jnum <arg>] [-g|--genomesize <arg>] [--bioproject <arg>] [--species <arg>] [--accession <arg>] [--query <arg>] [--subject <arg>] [-M|--minimum <arg>] [--(no-)reduction-reads] [--(no-)contigger] [--(no-)all-annotate] [--(no-)use-edges] [--(no-)coverage-check] [--(no-)resume] [-u|--(no-)circularize] [--(no-)test] [-v|--version] [-h|--help]
       polap <menu> help

menu: list, make-menus, or clean-menus
  assemble1, annotate, assemble2, flye-polishing,
  reset, total-length-long, find-genome-size, reduce-data,
  flye1, blast-genome, count-gene, select-reads, flye2,
  flye-polishing, check-coverage,
  prepare-polishing, polish,
  assemble,



Menu: assemble1

  polap assemble1 [-o|--outdir <arg>] [-l|--long-reads <arg>] [-a|--short-read1 <arg>] [-b|--short-read2 <arg>] [-m|--min-read-length <arg>] [-t|--threads <arg>] [-c|--coverage <arg>]

  or

  polap reset [-o|--outdir <arg>]

  polap total-length-long [-l|--long-reads <arg>]

  polap find-genome-size  [-a|--short-read1 <arg>] [-b|--short-read2 <arg>]

  polap reduce-data [-l|--long-reads <arg>] [-m|--min-read-length <arg>]

  polap flye1 [-t|--threads <arg>] [-c|--coverage <arg>] [-g|--genomesize <arg>]



Menu: annotate

  polap annotate [-i|--inum <arg>]

  or

  polap blast-genome [-i|--inum <arg>]

  polap count-genes [-i|--inum <arg>]



Menu: assemble2

  polap assemble2 [-o|--outdir <arg>] [-l|--long-reads <arg>] [-a|--short-read1 <arg>] [-b|--short-read2 <arg>] [-m|--min-read-length <arg>] [-t|--threads <arg>] [-c|--coverage <arg>]

  or

  polap select-reads [-i|--inum <arg>] [-j|--jnum <arg>] [-r|--pair-min <arg>] [-x|--bridge-min <arg>] [-w|--single-min <arg>]

  polap flye2 [-j|--jnum <arg>] [-t|--threads <arg>] [-c|--coverage <arg>]



Menu: polishing

  polap flye-polishing  [-j|--jnum <arg>] [-t|--threads <arg>] [-c|--coverage <arg>]

  polap prepare-polishing  [-a|--short-read1 <arg>] [-b|--short-read2 <arg>]

  polap polish [-p|--unpolished-fasta <arg>] [-f|--final-assembly <arg>]



Options:

  -o, --outdir: output folder name (default: o)

  -l, --long-reads: long-reads data file in fastq format (default: 'l.fq')

  -a, --short-read1: short-read fastq file 1 (default: 's1.fq')

  -b, --short-read2: short-read fastq file 2 (default: 's2.fq')

  -p, --unpolished-fasta: polishing sequence in fasta format (default: 'mt.0.fasta')

  -f, --final-assembly: final assembly in fasta format (default: 'mt.1.fa')

  -m, --min-read-length: minimum length of long reads (default: '3000')

  -t, --threads: number of CPUs (default: '56')

  -c, --coverage: coverage for the 2nd assembly (default: '30')

  -r, --pair-min: minimum mapped bases or PAF 11th column (default: '3000')

  -x, --bridge-min: minimum bridging read length or PAF 7th column (default: '3000')

  -w, --single-min: minimum mapped bases or PAF 11th column (default: '3000')

  -i, --inum: previous output number of organelle-genome assembly (default: '0')

  -j, --jnum: current output number of organelle-genome assembly (default: '1')

  -g, --genomesize: expected genome size (no default)

  -u, --circularize, --no-circularize: circularize a contig (off by default)

  -v, --version: Prints version

  -h, --help: Prints help



Places your long-read and short-read files at a folder.

long-read file [l.fq]

short-read files [s1.fq] and [s2.fq]

Execute: polap reset