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).

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.


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.


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