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Article History

Received: 16 October 2018

Accepted: 14 January 2019

First Online: 28 January 2019

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: The authors declared that they have no competing interests.

: The following terms, genome fraction, N50, number of contigs, misassemblies and local misassemblies, are defined by QUAST []Genome fraction “is the total number of aligned bases in the reference, divided by the genome size. A base in the reference genome is counted as aligned if there is at least one contig with at least one alignment to this base. Contigs from repeat regions may map to multiple places, and thus may be counted multiple times in this quantity.”N50 “is the contig length such that using longer or equal length contigs produces half (50%) of the bases of the assembly. Usually there is no value that produces exactly 50%, so the technical definition is the maximum length x such that using contigs of length at least x accounts for at least 50% of the total assembly length.”Number of contigs “is the total number of contigs in the assembly that have size greater than or equal to 0 bp.”Misassemblies “is the number of positions in the assembled contigs where the left flanking sequence aligns over 1 kbp away from the right flanking sequence on the reference (relocation) or they overlap on more than 1 kbp (relocation) or flanking sequences align on different strands (inversion) or different chromosomes (translocation).”Local misassemblies “A local misassembly has two or more distinct alignments covering the breakpoint, the gap between left and right flanking sequences is less than 1 kbp and the left and right flanking sequences both are on the same strand of the same chromosome of the reference genome.”

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