Contents of this Version_2.6 directory:
=======================================

If you wish to do assembly or mapping using the Newbler software, then download items (1), (2) and (3) from the list below:


  (1) DataAnalysis_2.6_All.tgz = Newbler assembler, mapper, Amplicon variant analyser, and sffinfo/sfffile software. Runs on Linux ONLY.

  (2) Manual-v2.6_Overview_May2011.pdf   = Overview of roche software, including sffinfo, sfffile

  (3) Manual-v2.6_PartC_Assembly_and_Mapping_May2011.pdf   = PDF file of Manual for Newbler Assembly and Mapping programs.

  (4) Manual-v2.6_PartD_AmpliconVariantAnalyzer_May2011.pdf  = PDF file of manual for the Amplican Variant Analyser.

  (5) Documentation_2.6_All_as_many_html_pages.tgz   = Documentation as many HTML files.


This software should install without problem on Fedora, Redhat and CentOS versions of Linux.


However, on Ubuntu you may receive an error message during installation. A work-around is:

(a) On Ubuntu, the "Nixstaller" installer used in the installation package will probably stop with the following error:

    Cannot execute command: type rocks2>&1

A work-around is to create a link so rocks always returns true:
 
     ln -s /bin/true ~/bin/rocks

     ( for more info see: http://seqanswers.com/forums/showthread.php?t=8944 post number '#9' )


(b) For the Newbler assembler itself there are both 64 bit and 32-bit versions in the one package, but the GUI part of the Roche
software seems to be only 32-bit, so the installation may complain about:

     "libraries not found : zlib.i386, libXi.i386, libXtst.i386, libXaw.i386"

On Ubuntu, to install these 32-bit libraries, you can use:
 
    sudo apt-get install ia32-libs




To run the Newbler assembler from the command-line, typically use:

(a) For Genome data:
    runAssembly -urt -het  -o assembly1  reads.sff
  where: "-urt" means "use read tips" to extend contigs across low coverage regions,
         "-het" is for reads from heterogenous sample -eg. from several individuals or diploid. 

(b) For Transcriptome data:
    runAssembly -urt -cdna -vt AdaptersToTrimFromReads.fna -o assembly1  reads.sff
  where: "-cdna" indicates reads are cDNA, so consider alternative splicing, and large reange of coverage.
         "-vt .." to trim adapters, such as MINT or SMART adapters used to synthesis the cDNA, from the reasd before assembly.

Several additional options can be use, such as "-vs ScreeningFile.fna" can optionally be used. See manual for more details.