Banana Slug Genomics

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====== Newbler assembly of POG ======
====== Overview ======
Outlines how Kevin assembled 454 data of Pyrobaculum oguniense (POG) using Newbler 2.3 version.  

===== Key points =====

  * Kevin installed Newbler 2.3 version in Campusrocks cluster under /campusdata/BME235/programs/DataAnalysis_2.3.
  * Newbler GUI is not installed as it has some issues with unpacking.
  * All the assemblies should be listed under /campusdata/BME235/assemblies.
  * Kevin ran the assembly tool on POG 454 data under /campusdata/BME235/assemblies/Pog.
  * The README file in the directory contains important information about the assembly.
  * Info about tools installed is listed in bioinformatic_tools [[https://banana-slug.soe.ucsc.edu/bioinformatic_tools:gs_de_novo_assembler | GS De Novo Assembler]]. Info about how to run the De novo as well as Mapping assembly tools is also included there.
  * Currently tools are installed under /campusdata/BME235/bin/old_Newbler/.
  * Its better to run the tool in the current working directory.
  * Tools with prefix "gs" are not supposed to be run directly.
  * Newbler assembly tools take .sff (color space and quality data) files as input and converts them into .fna (fasta file with nucleotide information) files.
  * Good only with 454 data, is not good on reads < 50bp. 
  * Example to run the tools on data is shown below. The code is taken from [[https://banana-slug.soe.ucsc.edu/bioinformatic_tools:gs_de_novo_assembler | GS De Novo Assembler]].
    <code>
newAssembly .
addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ01.sff
addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ02.sff
runProject -e 50 .
</code>
  * -e 50 is an important parameter -> implies expected coverage and it defaults to 50.
Banana Slug Genomics

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