I am working on fungal genome assembly using long reads and I am getting lots of misassemblies. Assembly was made using NextDenovo, which made 11 contigs with lots of misassemblies. stats are as follows:
Largest contig = 8126790
N50 = 5981938
misassemblies = 1939
I applied nextPolish as well but nothing improved. I m just wondering how can I improve this ??
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hafiz.talhamalik
Which reads ? I would try preferably flye, or shasta, which are both easy to install and run
I did try shasta but will try flye as wel.. just in case if misassemblies are still there how to overcome them ??
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How are misassemblies identified? Have you compared the number with another assembler such as Flye recommended below? (it is fast and easy to use even just for this test)
misassemblies were identified using quast and closest specie was used as a reference. I tried shasta, canu and NextDenovo for assemblies. Others had more misassemblies and more number of contigs, low n50 as well
With the next closest species as a reference these 'missassemblies' could just be genuine differences.