A meta-assembler that merges two assemblies created using long reads, or long reads and long+short reads. In reality it can merge any two sequences. That way, quickmerge can also be used to manually assemble ultra-long reads (as produced by Oxford nanopore). [link]

SVMU (Structural Variants from MUmmer)

SVMU can be used to identify all differences between two genomes. It annotates large scale structural differences, as well as small indels and SNPs. [link]


A comparative genome assembly scaffolding tool. It scaffolds contigs of one assembly based on another. Often, running mscaffolder on a assembly prior to running SVMU is helpful. [link]


mlift is genomic coordinate liftover tool based on MUMmer. It can lift coordinates of sequence features that span as little as 1 nucleotide. [link]

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