Banana Slug Genomics

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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

Installed and being tested 

== 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.

A Makefile that illustrates the use of the SunGrid to avoid running on the head node is shown in /campusdata/BME235/assemblies/Pog/newbler-assembly1/Makefile

== 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>
Banana Slug Genomics

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