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racon

  • scenario: scaffold in FASTA, reads in FASTQ format and alignments between the reads and the contigs in SAM format.

pilon

  • scenario: scaffold in FASTA, shortreads in FASTQ format and alignments between the reads and the contigs in SAM format.

nanopolish

  • scenario: scaffold in FASTA, reads in FASTQ format and alignments between the reads and the contigs in SAM format.

  • info nanopolish variants --consensus: calculate an improved consensus sequence for a draft genome assembly