Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-04-11T01:40:13.683Z
Answers.Text: 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 ?
Answers.UserDisplayName: LoveVirology
Answers.ContentLicense: CC BY-SA 4.0
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Answers.Text: `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.
Answers.UserDisplayName: Daniel Standage
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Answers.CreationDate: 2019-04-10T19:52:57.977Z
Answers.LastActivityDate: 2019-04-10T19:52:57.977Z
Answers.UserDisplayName: Daniel Standage
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-10T20:39:37.013Z
Comments.Text: Cross-posted on biostars: https://www.biostars.org/p/374352/
Comments.UserDisplayName: Ram RS
Tags: <sam><genome><assembly>
Title: Consensus sequence from SAM or BAM file?
ThreadText: # Consensus sequence from SAM or BAM file?
  
  (Asked by: username_0 on 2019-04-10)
  
  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 ?
  
  **Tags:** sam, genome, assembly
  
  > **Comments:**
  > **username_1**: Cross-posted on biostars: https://www.biostars.org/p/374352/  
  
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  ## 1 answers
  
  ### Answer by username_2 on 2019-04-10. Score: 1
  
  A few years ago I used AlignGraph ([paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058956/) and [code](https://github.com/baoe/AlignGraph)) 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](https://www.ncbi.nlm.nih.gov/pubmed?linkname=pubmed_pubmed_citedin&from_uid=24932000).
  
  > **Comments:**
  > **username_0**: 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 ?  
  > **username_2**: `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.  
  
  ---
  
  