Does anyone know what would be an easy and good way to assemble a bacterial plasmid genome (5-20kb) from Illumina reads that are 150 bases long? I have at least 1000x coverage. Some time ago I tried to use soap denovo and velvet but didn't get good results so I turned to mapping reads to a reference since I had the reference. Now I don't have a reference and would need de novo assembler. The plasmids don't contain repeats.
Hi, I developed a new de novo assembler for plastids and it should assemble the genome in one circular contig. I will upload the assembler in the next few weeks if you would be interested: https://github.com/ndierckx/NOVOPlasty
I could already upload a beta version next week, probably some bugs, but all tests were successful. I assembled 10 chloroplasts, all in one contig and within 30 min. The high coverage is no problem for this assembler and you don't need any reference. For the paper I assembled the chloroplast of Arabidopsis and rice, they were both 100 % accurate, so you should obtain a high quality assembly. I haven't tested it on plasmids but it's the same concept so should work..