text: user1593: I'm a computer scientist working with biologists at a small school that doesn't have dedicated bioinformatics staff. I apologize if I use incorrect terminology since I have limited bioinformatics background.
  Our biology staff is studying a soil sample that has been sequenced. The resulting sequences (in the hundreds of millions) were analyzed using mg-rast, but they didn't seem to have a high confidence in the results.
  I've been asked to help analyze these sequences. I setup a local instance of NCBI blast, but it was far too slow to analyze that many sequences. We moved on to using BLAT. They've requested we use the nt database from NCBI. I converted the nt FASTA file to 2bit file, splitting the files into small chunks.
  gfServer seems to have limitations however. When I run gfServer, I get the following error while gfServer attempts to start.
  
  Exceeding 4 billion bases, sorry gfServer can't handle that.
  
  Is it possible to use the full nt database using BLAT? Is there an alternative to BLAT that can handle that many sequences?
  
  user73: I'd recommend having a go with either OneCodex (commercial / Freemium) or Centrifuge.
  Chris Mason's lab has recently looked at metagenomic classification and OneCodex gave the most accurate result.
  Centrifuge uses Burrows-Wheeler lookups, but hasn't yet been compared by the Mason Lab.
  
original_text: 1593: <p>I'm a computer scientist working with biologists at a small school that doesn't have dedicated bioinformatics staff. I apologize if I use incorrect terminology since I have limited bioinformatics background.</p>
  
  <p>Our biology staff is studying a soil sample that has been sequenced. The resulting sequences (in the hundreds of millions) were analyzed using mg-rast, but they didn't seem to have a high confidence in the results.</p>
  
  <p>I've been asked to help analyze these sequences. I setup a local instance of NCBI blast, but it was far too slow to analyze that many sequences. We moved on to using BLAT. They've requested we use the nt database from NCBI. I converted the nt FASTA file to 2bit file, splitting the files into small chunks.</p>
  
  <p>gfServer seems to have limitations however. When I run gfServer, I get the following error while gfServer attempts to start.</p>
  
  <blockquote>
    <p>Exceeding 4 billion bases, sorry gfServer can't handle that.</p>
  </blockquote>
  
  <p>Is it possible to use the full nt database using BLAT? Is there an alternative to BLAT that can handle that many sequences?</p>
   73: <p>I'd recommend having a go with either <a href="https://onecodex.com/" rel="nofollow noreferrer">OneCodex</a> (commercial / Freemium) or <a href="http://ccb.jhu.edu/software/centrifuge/" rel="nofollow noreferrer">Centrifuge</a>.</p>
  
  <p>Chris Mason's lab has <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1299-7" rel="nofollow noreferrer">recently looked at metagenomic classification</a> and OneCodex gave the most accurate result.</p>
  
  <p>Centrifuge uses <a href="http://genome.cshlp.org/content/26/12/1721.full" rel="nofollow noreferrer">Burrows-Wheeler lookups</a>, but hasn't yet been compared by the Mason Lab.</p>
  