text: user1684: 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 ?
  
  user96: 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.
  
original_text: 1684: <p>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 ?</p>
   96: <p>A few years ago I used AlignGraph (<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058956/" rel="nofollow noreferrer">paper</a> and <a href="https://github.com/baoe/AlignGraph" rel="nofollow noreferrer">code</a>) 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.</p>
  
  <p>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 <a href="https://www.ncbi.nlm.nih.gov/pubmed?linkname=pubmed_pubmed_citedin&amp;from_uid=24932000" rel="nofollow noreferrer">articles that cite the AlignGraph paper</a>.</p>
  