Hi, I'm a new bioinformatician and wondering if what I want is possible or even logical.
I sequenced (slightly) mutant E coli, genome should be approx 4.6GB. I used SPADES to do a de novo assembly from my paired sequencing but end with 2000 contigs and the largest is 25kb. My sequenced bacteria should be very similar to a published genome. Is there a way to use this published genome to help build my sequenced contigs/scaffolds rather than only using spades to do de novo assembly? Reading the spades manual didn't really clear it up for me.
spades.py -1 Merged_MG1655_runs1and2_R1.fastq.gz -2 Merged_MG1655_runs1and2_R2.fastq.gz -o Merged_MG1655_runs1and2_spades_output --only-assembler
Is what I was using. Thanks very much, any help much appreciated.