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..
**Getting this error: /Users/lindakohn/Desktop/tools/SPAdes-3.7.1-Darwin/bin/spades.py -k 21,33,55,77 --careful --only-assembler --pe<#>-12 <euro_plasmid_r1_paired.fastq euro_plasmid_r2_paired.fastq=""> --pe<#>-s1 <euro_plasmid_r1_unpaired.fastq> --pe<#>-s2 <euro_plasmid_r2_unpaired.fastq> -o Euro_plasmid_spades_output
-bash: syntax error near unexpected token `newline' what is wrong with the command?**