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README.md

Racon + Minimap2 Container

This container combines Racon and Minimap2 for efficient polishing and alignment in long-read assembly workflows.

Tools Included

  • Racon: Polishes long-read assemblies.
  • Minimap2: Generates alignments for use with Racon and other polishing tools.

Code Repositories

Basic Information

Racon

  • Executable: racon
  • Help: racon -h
  • Version: racon -v
  • Description:

    Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods that do not include a consensus step.

Minimap2

  • Executable: minimap2
  • Help: minimap2 -h
  • Version: minimap2 --version
  • Description:

    Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.

Example Usage

# Racon general
racon <sequences> <overlaps> <target sequences>

# more specific
racon --match 8 --mismatch -6 --gap -8 --window-length 500 --threads {threads} {input.reads} {input.alignment} {input.assembly}

#Combined Racon and Minimap2 Workflow

#Align Reads to Assembly Using Minimap2:
minimap2 -x map-ont <assembly.fasta> <reads.fastq> > overlaps.paf

#polish assembly using Racon
racon --threads {threads} <reads.fastq> overlaps.paf <assembly.fasta> > polished_assembly.fasta