Answers.Body: <p>Here are a couple books I'd recommend:</p>
  
  <p>Dan Gusfield's <a href="https://www.cambridge.org/core/books/algorithms-on-strings-trees-and-sequences/F0B095049C7E6EF5356F0A26686C20D3" rel="nofollow noreferrer">Algorithms on Strings, Trees, and Sequences</a> is a deep and wide treatment of aligning, searching, and processing strings, trees, and sequences.</p>
  
  <p>Warren Ewens' <a href="http://www.springer.com/gp/book/9780387400822" rel="nofollow noreferrer">Statistical Methods in Bioinformatics</a> devotes a chapter to BLAST and the math underneath it.</p>
  
  <p><em>Edit</em> - Another book that may be useful for some mathematical underpinnings would be Michael S. Waterman's <a href="https://doi.org/10.1002/(SICI)1097-0258(19961030)15:20%3C2264::AID-SIM386%3E3.0.CO;2-7" rel="nofollow noreferrer">Introduction to Computational Biology</a>.</p>
  
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Answers.Text: I agree that algorithm books, like Gusfield's, are hugely important. Personally though, I have that covered decently already.
Answers.UserDisplayName: Ólavur
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Answers.Text: The Waterman book looks quite interesting, it has some material that I haven't seen in other books.
Answers.UserDisplayName: Ólavur
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Answers.LastEditDate: 2018-03-27T19:18:55.387Z
Answers.UserDisplayName: Alex Reynolds
Answers.Body: <p><a href="https://rads.stackoverflow.com/amzn/click/1118581784" rel="nofollow noreferrer">Bioinformatics and Functional Genomics</a> by Jonathan Pevsner is a good one, he goes over the biology as well as how the algorithms work, and provides real-world examples.</p>
  
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Answers.CreationDate: 2018-04-05T12:11:42.760Z
Answers.Text: This one is very nice, a colleague of mine happens to have it. It doesn't seem to go into much detail with the math and algorithms though (which is not a deal breaker or anything), probably because it's targeted mostly at biology students. I think it has a very nice way of tying the algorithms to the biological context. Perhaps this book is a good introduction, and to get more mathematical details one can read papers on BLAST, aligners such as BWA, and so on.
Answers.UserDisplayName: Ólavur
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Answers.UserDisplayName: Imer Muhović
Answers.Body: <p>If you're interested in variant calling, I just co-authored an O'Reilly book called <a href="https://oreil.ly/genomics-cloud" rel="nofollow noreferrer">Genomics in the Cloud</a> that covers the GATK Best Practices from a scientific standpoint (germline and somatic short variants + somatic copy number alterations), as well as technical considerations like how to run it efficiently at scale (that's where the cloud part comes in). </p>
  
  <p>You can read more about it on the GATK blog; there's an <a href="https://gatk.broadinstitute.org/hc/en-us/articles/360042408831" rel="nofollow noreferrer">announcement</a> and a second <a href="https://gatk.broadinstitute.org/hc/en-us/articles/360042106212" rel="nofollow noreferrer">more personal blog post</a> that I wrote to explain how I approached the topic. Happy to discuss more if you're interested.</p>
  
  <p>Oh and you can preview the first few chapters for free <a href="https://rads.stackoverflow.com/amzn/click/com/1491975199" rel="nofollow noreferrer" rel="nofollow noreferrer">on Amazon</a> if you like. </p>
  
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Answers.UserDisplayName: Geraldine_VdAuwera
Body: <p>I'm looking for a book about bioinformatics algorithms, such as alignment, BLAST search, and variant calling.</p>
  
  <p>I'm hoping reading about this subject will give me a deeper understanding of the foundations of bioinformatics, and I'm also interested in developing my own tools and algorithms for sequence and variant analysis. I studied applied mathematics and computer science at university, so I don't shy away from math-heavy books.</p>
  
  <p>I've listed some candidates below. </p>
  
  <ul>
  <li><a href="https://rads.stackoverflow.com/amzn/click/0521629713" rel="noreferrer">Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleid Acids, 1st edition, Durbin et al. 1998</a></li>
  <li><a href="https://rads.stackoverflow.com/amzn/click/0262101068" rel="noreferrer">An Introduction to Bioinformatics Algorithms, 1st edition, Jones et al. 2004</a></li>
  <li><a href="https://www.amazon.co.uk/Algorithms-Bioinformatics-Introduction-Mathematical-Computational/dp/1420070339/ref=sr_1_3?ie=UTF8&amp;qid=1517212543&amp;sr=8-3&amp;keywords=bioinformatics+algorithms" rel="noreferrer">Algorithms in Bioinformatics: A Practical Introduction, Sung 2010</a></li>
  </ul>
  
  <p>Durbin et al. is quite old, Sung is the newest. </p>
  
  <p>I am looking for books with:</p>
  
  <ul>
  <li>material (algorithms) on alignment, assembly, and variant calling if possible. </li>
  <li>New books are preferred</li>
  </ul>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-03-27T14:36:56.157Z
Comments.Text: "Biological Sequence Analysis" is excellent, you say it's old but it's been re-printed many times with edits and is still very relevant. My edition is the 10 re-reprinting from 2010, they may be an even more recent one
Comments.UserDisplayName: Chris_Rands
Tags: <phylogenetics><variant-calling><sequence-analysis><algorithms><literature-search>
Title: Books on bioinformatics algorithms
ThreadText: # Books on bioinformatics algorithms
  
  (Asked by: username_0 on 2018-03-27)
  
  I'm looking for a book about bioinformatics algorithms, such as alignment, BLAST search, and variant calling.
  
  I'm hoping reading about this subject will give me a deeper understanding of the foundations of bioinformatics, and I'm also interested in developing my own tools and algorithms for sequence and variant analysis. I studied applied mathematics and computer science at university, so I don't shy away from math-heavy books.
  
  I've listed some candidates below.
  
  * [Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleid Acids, 1st edition, Durbin et al. 1998](https://rads.stackoverflow.com/amzn/click/0521629713)
  * [An Introduction to Bioinformatics Algorithms, 1st edition, Jones et al. 2004](https://rads.stackoverflow.com/amzn/click/0262101068)
  * [Algorithms in Bioinformatics: A Practical Introduction, Sung 2010](https://www.amazon.co.uk/Algorithms-Bioinformatics-Introduction-Mathematical-Computational/dp/1420070339/ref=sr_1_3?ie=UTF8&qid=1517212543&sr=8-3&keywords=bioinformatics+algorithms)
  
  Durbin et al. is quite old, Sung is the newest.
  
  I am looking for books with:
  
  * material (algorithms) on alignment, assembly, and variant calling if possible.
  * New books are preferred
  
  **Tags:** phylogenetics, variant-calling, sequence-analysis, algorithms, literature-search
  
  > **Comments:**
  > **username_1**: "Biological Sequence Analysis" is excellent, you say it's old but it's been re-printed many times with edits and is still very relevant. My edition is the 10 re-reprinting from 2010, they may be an even more recent one  
  
  ---
  
  ## 3 answers
  
  ### Answer by username_2 on 2018-03-27. Score: 4
  
  Here are a couple books I'd recommend:
  
  Dan Gusfield's [Algorithms on Strings, Trees, and Sequences](https://www.cambridge.org/core/books/algorithms-on-strings-trees-and-sequences/F0B095049C7E6EF5356F0A26686C20D3) is a deep and wide treatment of aligning, searching, and processing strings, trees, and sequences.
  
  Warren Ewens' [Statistical Methods in Bioinformatics](http://www.springer.com/gp/book/9780387400822) devotes a chapter to BLAST and the math underneath it.
  
  *Edit* - Another book that may be useful for some mathematical underpinnings would be Michael S. Waterman's [Introduction to Computational Biology](https://doi.org/10.1002/(SICI)1097-0258(19961030)15:20%3C2264::AID-SIM386%3E3.0.CO;2-7).
  
  > **Comments:**
  > **username_0**: I agree that algorithm books, like Gusfield's, are hugely important. Personally though, I have that covered decently already.  
  > **username_0**: The Waterman book looks quite interesting, it has some material that I haven't seen in other books.  
  
  ---
  
  ### Answer by username_3 on 2018-04-03. Score: 3
  
  [Bioinformatics and Functional Genomics](https://rads.stackoverflow.com/amzn/click/1118581784) by Jonathan Pevsner is a good one, he goes over the biology as well as how the algorithms work, and provides real-world examples.
  
  > **Comments:**
  > **username_0**: This one is very nice, a colleague of mine happens to have it. It doesn't seem to go into much detail with the math and algorithms though (which is not a deal breaker or anything), probably because it's targeted mostly at biology students. I think it has a very nice way of tying the algorithms to the biological context. Perhaps this book is a good introduction, and to get more mathematical details one can read papers on BLAST, aligners such as BWA, and so on.  
  
  ---
  
  ### Answer by username_4 on 2020-04-22. Score: 3
  
  If you're interested in variant calling, I just co-authored an O'Reilly book called [Genomics in the Cloud](https://oreil.ly/genomics-cloud) that covers the GATK Best Practices from a scientific standpoint (germline and somatic short variants + somatic copy number alterations), as well as technical considerations like how to run it efficiently at scale (that's where the cloud part comes in).
  
  You can read more about it on the GATK blog; there's an [announcement](https://gatk.broadinstitute.org/hc/en-us/articles/360042408831) and a second [more personal blog post](https://gatk.broadinstitute.org/hc/en-us/articles/360042106212) that I wrote to explain how I approached the topic. Happy to discuss more if you're interested.
  
  Oh and you can preview the first few chapters for free [on Amazon](https://rads.stackoverflow.com/amzn/click/com/1491975199) if you like.
  
  
  ---
  
  