text: user1296: 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
  An Introduction to Bioinformatics Algorithms, 1st edition, Jones et al. 2004
  Algorithms in Bioinformatics: A Practical Introduction, Sung 2010
  
  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
  
  
  user369: Bioinformatics and Functional Genomics by Jonathan Pevsner is a good one, he goes over the biology as well as how the algorithms work, and provides real-world examples.
  
  user2776: If you're interested in variant calling, I just co-authored an O'Reilly book called Genomics in the 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 and a second more personal blog post 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 if you like. 
  
  user776: Here are a couple books I'd recommend:
  Dan Gusfield's Algorithms on Strings, Trees, and Sequences is a deep and wide treatment of aligning, searching, and processing strings, trees, and sequences.
  Warren Ewens' Statistical Methods in Bioinformatics 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.
  
original_text: 1296: <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>
   369: <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>
   2776: <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>
   776: <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>
  