Tag: MUMmer

Has anyone here used the MAC tool for merging assemblies?

Has anyone here used the MAC tool for merging assemblies? 0 I’m relatively new to whole genome work and have been exploring various tools for assembling/mapping genomes. I’ve read that not all assembly tools/programs are created equal and often times it is valuable to assess assemblies from multiple tools for…

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How to get the sequence differences between multiple bacterial genomes

How to get the sequence differences between multiple bacterial genomes 1 I am working on some closely related bacterial species (complete genomes from NCBI). I would like to extract the sequence differences between them. To be more specific, I want to find unique sequences (50 -100 nts) in each of…

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Is it possible to do mummerplot with reference and query sequences that have many contigs?

Is it possible to do mummerplot with reference and query sequences that have many contigs? 0 Hi, I have a reference genome that has 9 contigs and query genome that has 56 contigs. They both has more than 99 % identical nucleotides. I tried to make mummerplot but got really…

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Mapping transcripts to mitogenome

Mapping transcripts to mitogenome 0 I have performed de novo assembly of a plant mitogenome (non-model plant). In addition, I also perform de novo transcriptome assembly of this particular plant species. How to verify if the mitogenome assembly is correct making use of the RNA-Seq data? Should I align my…

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