Could anyone suggest me an easiest way to perform pairwise sequence alignment wherein my query sequence is the sequencing reads obtained from NGS and the subject sequence is a constant part expected to be found on the reads. So, i need to have a score and length of alignment as parameters to screen and filter. I would like to execute Smith-Waterman algorithm. I tried using python but it is getting complicated for me to find EMBOSS suite (which I finally downloaded) but then cannot execute it from python (tried WaterCommandline). And I am not even sure that this will give me a score and alignment length if I successfully manage to execute it. I am looking up in R now to see if it is possible and reiterate all the reads against a subject sequence. Then, I would like to splice the query sequence and store it in a file in a fasta format following the sequence alignment. Any ideas on how to conveniently do this will be appreciated.
I used blast+ for a similar task and it worked fairly well. You'll need to convert the .bam/.sam file to a fasta file first but the results in tabulated format are really easy to filter based on score or alignment length.
Not sure to understand what you mean by "splicing" the query.