This Python Flask app will take a reference plasmid genome Fasta file and 2 paired read NGS FastQ files and align them. 
The program BWA mem is used for aligning the reads, Samtools for a consensus sequence and Clustal Omega for the alignment of the reference sequence to the consensus sequence.
A graphic representation of the alignment against the reference sequence is output along with a downloadable Fasta file of the consensus sequence. This output will not include insertions as the consensus sequence output from BWA mem does not include them.