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=== NEWBLER a.k.a. GS De Novo Assembler Software === Newbler is a proprietary assembler provided by 454 Roche. It works in flow-space to reduce the impact of its most common sequencing error (uncertainty about the length of homopolymers).\\ It claims it can assemble a 3GB genome in one day and can use paired-end information to construct scaffolds from contigs. Currently the paired-end data must have at least 50 bases in each end, so only 454 paired-end libraries are accepted---it would be good if they relaxed that constraint so that their data could be mixed with data from other platforms. Roche 454 info about [[http://454.com/products-solutions/analysis-tools/gs-de-novo-assembler.asp|Newbler]] Wiki [[http://en.wikipedia.org/wiki/Newbler|article]].\\ Documentation: [[http://xyala.cap.ed.ac.uk/Gene_Pool/454_software/]] (probably not supposed to be free on the web, though...)\\ First description: [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1464427/ ]]\\ A review article with a decent description: [[http://www.ncbi.nlm.nih.gov/pubmed/20211242]] == Installation on campusrocks == The following tools were installed on BME235/bin/ on 15 April 2010: * addRun * createProject * doAmplicon * fnafile * getProjAlignData * gsAmplicon * gsAssembler * gsMapper * newAssembly * newbler * newMapping * removeRun * runAssembly * runMapping * runProject * setRef * sff2scf * sfffile * sffinfo * sffrescore * stopRun (but I haven't tested them yet --- //[[karplus@soe.ucsc.edu|Kevin Karplus]] 2010/04/15 16:02//) BUG: I installed the old version...I'll have to try again with the 2.3 version. --- //[[karplus@soe.ucsc.edu|Kevin Karplus]] 2010/04/15 18:36// == De novo assembly == The standard commands for de novo assembly are to create a new directory, and in that directory create a Makefile that includes a target to execute the following commands: <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> Of course, different sff files will be used on different runs. == Mapping to existing genome == Many genomes can be assembled by mapping reads to an existing "close enough" genome. This "close-enough" genome can even be one assembled by Newbler ab initio! The standard commands for mapping assembly are to create a new directory, and in that directory create a Makefile that includes a target to execute the following commands: <code> newMapping . setRef . /campusdata/BME235/data/Pog/finished/Pog.chr.v3.fa setRef . /campusdata/BME235/data/Pog/finished/Pog.ece.v3.fa addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ01.sff addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ02.sff runProject -e 50 . </code>
