We have sequenced two plasmids with a Novaseq machine (reads length of 100 bp, paired end).
For one of them, we have aligned the reads against the reference genome using BWA-mem and, as the reads mapped across the full length of the reference genome, we have extracted the sequence of the plasmid on IGV (with the feature extract consensus sequence):
However, for the other sequence, the alignment on IGV showed that the reads mapped only against a portion of the reference genome.
Therefore, it would be meaningless to extract the consensus sequence from IGV. We then sought to perform denovo assembly using Spades. We ran the following command
path/to/spades.py --careful -1 /path/Read1_001.fastq.gz -2 /path/toRead2_001.fastq.gz -o /path/to/outdir
The thing is that Spades outputs, among others, a
scaffold.fasta and a
contigs,fasta file. I was now wondering how (if) is it possible to get the continuous plasmid sequence from the Spades output?