Hi, I have recently sequenced mitochondrial genomes of parasitic nematodes that were amplified by long range PCR. I am looking for suggestions for the best program to assemble these reads (paired end reads, 2x75, illumina Nextera XT, v3 reagents). So far i have tried the free SPAdes genome analyzer available on illumina, DNASTAR lasergene (seqman ngen), and trinity. Trinity gave the best results, but it is optimized for transcriptomics, and I do not think it has given optimal results.
Any suggestions are appreciated!
If you have amplified just mitogenome (not transcriptome) you could use almost any program. It should be complete and assemble easily because you have many copies. You could use geneious, clc genomics workbench or sequencher, for example.
I have been working with them and if you have good sequences there wouldn´t be any problem.
To anotate the mitogenome you could use. DOGMA or MITOS servers.
Have a look to my papers ;-)
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