Consensus sequence from SAM or BAM file? I am trying to perform reference-based assembly. Most of the tutorials teach how to create a bam file and view alignemnts in IGV or Tablet. But, I want a assembled genome sequence in fasta format. How can I do that ? Is there any tool or linux syntax available for this purpose ?
A few years ago I used AlignGraph (paper and code) for a task like this. I gave AlignGraph my raw reads, so I'm not sure if it accepts SAM/BAM input or if you have to go back to the original Fastq reads.

I'm not sure if any related/improved tools have been published since AlignGraph. Internet searches for "reference-guided assembly" return mostly transcriptome assembly tools. It might be worth looking for articles that cite the AlignGraph paper.