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Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step, such as Miniasm. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods.

Racon takes as input only three files: the raw contig FASTA, the original raw reads in FASTQ format and an overlap file in PAF or MHAP format containing overlaps between the reads and the contigs. Overlaps can be generated quickly using Minimap and piped through to Racon (see example usage below). Racon then reads the overlaps, filters them, and aligns the region defined by each overlap.

Environment Modules

Run module spider racon to find out what environment modules are available for this application.

System Variables

  • HPC_RACON_DIR - installation directory