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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 De novo tool 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> * Where, -e 50 is an important parameter -> implies expected coverage and it defaults to 50.
