Tuesday, May 31, 2011

minimus2-blat

I'm currently playing around with putting together an assembly pipeline that will merge the contigs generated from assembly of same input data with different parameters.
My current assembler of choice for working with 454 data is Newbler.
It can only handle input reads as long as 2000 bases. Shredding the initial contigs is an option but I have been told that Newbler has difficulty putting these contigs back together again.
Minimus2, part of the AMOS package, is made just for that. The latest addition to the minimus tools is minimus2-blat, which is possibly the fastest of the three minimus2 tools.

Here's how to install it:
mkdir AMOS
cd AMOS
cvs -d:pserver:anonymous@amos.cvs.sourceforge.net:/cvsroot/amos login
cvs -z3 -d:pserver:anonymous@amos.cvs.sourceforge.net:/cvsroot/amos co -P AMOS
./bootstrap
./configure
make
make install
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4 comments:

  1. AuthorJune 1, 2011 at 7:40 AM

    Hope you could get minmius2-blat to run on your dataset without any errors.

    ReplyDelete
  2. Daniel BramiJune 2, 2011 at 12:13 PM

    Hi Nagarjun,

    minmius2-blat never ran to completion. It seems the default overlap length of 40, which is then used as the tile parameter for blat is outside the '6-18' range that is allowed. Decreasing the parameter to 18 moves the pipeline along a bit but it then crashed when no output was generated during an intermediary step.

    Merging the assemblies using minimus2 (with nucmer) did complete. However my resulting merged assemblies are lot worse than 1 of my inputs.

    I will keep playing with these and post some results.

    ReplyDelete
  3. My_Two_CentsJune 29, 2012 at 9:04 AM

    Hi Nagarjun and Daniel,
    I ran into the same problem with minimus2-blat. The first error was, as Daniel suggested, in tile parameter and second problem was with 'blat2nucmer.pl' script being used in step 21 of 'minimus2-blat' program. find the blat2nucmer.pl (it might be in your /usr/local/bin folder) script change both print command in "blat2nucmer" subroutine as following.

    'print ($values[15+1])."\t".' --to--> print "".($values[15+1])."\t".

    I think, somehow braces "(" right after print is interpreted as some function, so i added "" before braces. It worked for me now.
    There was other problem where minimus2 and minimus2-blat could not find the nucmer and blat execulatbles. I had to change the path of those executable in minimus2 and minimus2-blat program to make it work.

    ReplyDelete
  4. UnknownJune 25, 2013 at 12:11 PM

    I get the errors that the BLAT and BOOST are missing when I try to compile amos. Where did you download BLAT and BOOST to make it work?

    Thanks

    ReplyDelete

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