Folks,
I am working on amplicon sequencing , with my 1st round of PCR amplifying only about few hundred exons I care about, sequences of which would be my reference fasta.
I am hoping to do Smith watermann(SW) for each read vs each reference and pick the one reference with max score as a match.
While there are ways to trick programs like Bfast and BWA, to do smith watermann, it would still be suboptimal if the mask based CAL does not catch on, reaches limit of CALS, or if even the best match is so poor that it cannot be reported.
I was wondering if there is a program/tool that does smith watermann (SW) directly and most importantly export alignments in SAM files?
I can do SW using pairwise align in R/ ghetto perl/bioperl scripts, however the main obstacle is conversion to SAM format output. Is there a way to sam conversion.
I am using pileups in SAMtools so I would have to pipe stuff into that eventually.
Thanks for your suggestions.
I am working on amplicon sequencing , with my 1st round of PCR amplifying only about few hundred exons I care about, sequences of which would be my reference fasta.
I am hoping to do Smith watermann(SW) for each read vs each reference and pick the one reference with max score as a match.
While there are ways to trick programs like Bfast and BWA, to do smith watermann, it would still be suboptimal if the mask based CAL does not catch on, reaches limit of CALS, or if even the best match is so poor that it cannot be reported.
I was wondering if there is a program/tool that does smith watermann (SW) directly and most importantly export alignments in SAM files?
I can do SW using pairwise align in R/ ghetto perl/bioperl scripts, however the main obstacle is conversion to SAM format output. Is there a way to sam conversion.
I am using pileups in SAMtools so I would have to pipe stuff into that eventually.
Thanks for your suggestions.