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…
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…
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…
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…
