I am still a newbie in genome assembly, so I don’t know if what I want to do is possible or makes sense.
I just did de novo assembly on bacterial Illumina PE with SPAdes. I end up with about 30 contigs.
I heard a lot of people usually map their original reads against their assembly to assess assembly quality.
I tried with Bowtie2, the job runs and gives a tabular file with the name of my contigs and then empty entries. But when I mapped my reads against a reference genome from NCBI, I end up with the reads names and then all entries ok.
What I am doing wrong?
Thank you for your time!