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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 ?

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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.

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  • $\begingroup$ It seems like AlignGraph takes reads in fasta format. Does it accept fastq format ? What tool do you use to convert fastq to fasta format ? $\endgroup$
    – L R Joshi
    Commented Apr 11, 2019 at 1:40
  • $\begingroup$ cat reads.fastq | paste - - - - | cut -f 1-2 | sed 's/^@/>/' | tr '\t' '\n' > reads.fasta. You can replace cat with gunzip -c if your Fastqs are compressed. $\endgroup$ Commented Apr 11, 2019 at 13:06

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