Hello,
I am doing de novo assembly of some E. coli genomes (~5 MB). The libraries were prepared using a Nextera XT kit, sequenced on an Illumina MiSeq, giving 150bp paired-end reads.
One of the genomes contains an already fully sequenced 90kB plasmid. The 'expected coverage' for this sample is only approximately 35X. I have tried to assemble this sample using Velvet with a wide range of kmer values (from 45-99).
When I aligned the assembled contigs back to the plasmid, I notice that the sections that hit the plasmid are generally fragmented amongst larger contigs (larger than the plasmid).
Does anybody have any advice they could share to avoid this plasmid and chromosome misassembly? Is it due to the low coverage (but I have seen this in a previous run with higher coverage)? Is it due to a possible difference in coverage (I'm not sure if the plasmid has a copy number greater than the genome)? Should I just move to a different assembler?
Any help and advice would be very much welcomed and appreciated!
Kind regards,
Heidi
I am doing de novo assembly of some E. coli genomes (~5 MB). The libraries were prepared using a Nextera XT kit, sequenced on an Illumina MiSeq, giving 150bp paired-end reads.
One of the genomes contains an already fully sequenced 90kB plasmid. The 'expected coverage' for this sample is only approximately 35X. I have tried to assemble this sample using Velvet with a wide range of kmer values (from 45-99).
When I aligned the assembled contigs back to the plasmid, I notice that the sections that hit the plasmid are generally fragmented amongst larger contigs (larger than the plasmid).
Does anybody have any advice they could share to avoid this plasmid and chromosome misassembly? Is it due to the low coverage (but I have seen this in a previous run with higher coverage)? Is it due to a possible difference in coverage (I'm not sure if the plasmid has a copy number greater than the genome)? Should I just move to a different assembler?
Any help and advice would be very much welcomed and appreciated!
Kind regards,
Heidi
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