Banana Slug Genomics

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==== List of Tools ====
Here is a list of the tools we are considering using for assembling and annotating the Banana Slug genome. Each of these listed tools will have their own page describing what the tool is supposed to do, and what we were able to get it to do. 

=== Pre-Processing tools ===
Tools used on reads before assembly to improve assembly quality
  * [[archive:bioinformatic_tools:seqprep|SeqPrep]]((https://github.com/jstjohn/SeqPrep)) Trim adapters/primers from ends of illumina reads, and merges paired illumina reads into singles if there is a user defined minimum overlap.
  * [[archive:bioinformatic_tools:jellyfish|JELLYFISH]]((http://www.cbcb.umd.edu/software/jellyfish/)) Do K-mer counting on reads
  * [[archive:bioinformatic_tools:quake|Quake]]((http://www.cbcb.umd.edu/software/quake/)) Do K-mer correction on reads (Can use JELLYFISH results as input)



=== Assembly Tools ===
The initial list of assembly tools was created from the [[wp>Sequence_assembly#Available_assemblers|Sequence Assembly]] page. However the links to the programs have been double checked, and some of them are different from those listed on the wikipedia page. --- //[[jstjohn@soe.ucsc.edu|John St. John]] 2010/03/29 20:02//

The only de-novo assemblers that can use Solid colorspace are Velvet (DBG) and Shorty (Overlap Concensus).
CLC bio’s de novo assembler uses Solid reads in a limited way for mate-paired resolution of contigs only.

[[http://gage.cbcb.umd.edu/index.html | Here]] is an analysis of assemblers that used many of the assembler we are looking into. It includes "recipes" for how they ran each assembler.

== Probably Open Source Tools == 
  * [[archive:bioinformatic_tools:phrap|Phrap]]((http://www.phrap.org/phredphrap/phrap.html))
  * [[archive:bioinformatic_tools:velvet|Velvet]]((http://www.ebi.ac.uk/~zerbino/velvet/))
  * [[archive:bioinformatic_tools:abyss|ABySS]]((http://www.bcgsc.ca/platform/bioinfo/software/abyss))
  * [[archive:bioinformatic_tools:allpaths|ALLPATHS]]((ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-3-0/)) 
  * [[archive:bioinformatic_tools:amos|AMOS]]((http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS_Getting_Started))
  * [[archive:bioinformatic_tools:arachne|Arachne]]((http://www.broadinstitute.org/crd/wiki/index.php/Arachne_Main_Page))
  * [[archive:bioinformatic_tools:cap3_pcap|CAP3/PCAP]]((http://seq.cs.iastate.edu/))
  * [[archive:bioinformatic_tools:celera|Celera]]((http://www.cbcb.umd.edu/research/CeleraAssembler.shtml))
  * [[archive:bioinformatic_tools:euler|Euler]]((http://nbcr.sdsc.edu/euler/))
  * [[archive:bioinformatic_tools:euler_sr|Euler-sr]]((http://euler-assembler.ucsd.edu/portal/))
  * [[archive:bioinformatic_tools:mira|MIRA]]((http://sourceforge.net/apps/mediawiki/mira-assembler/index.php?title=Main_Page))
  * [[archive:bioinformatic_tools:tigr|TIGR]]((ftp://ftp.jcvi.org/pub/software/assembler/))
  * [[archive:bioinformatic_tools:sharcgs|SHARCGS]]((http://sharcgs.molgen.mpg.de/))
  * [[archive:bioinformatic_tools:ssake|SSAKE]]((http://www.bcgsc.ca/platform/bioinfo/software/ssake))
  * [[bioinformatic_tools:staden_gap4|Staden gap4 package]]((http://staden.sourceforge.net/))
  * [[archive:bioinformatic_tools:vcake|VCAKE]]((http://sourceforge.net/projects/vcake/))
  * [[archive:bioinformatic_tools:phusion|Phusion]]((http://www.sanger.ac.uk/resources/software/phusion/))
  * [[archive:bioinformatic_tools:qsra|QSRA]]((http://qsra.cgrb.oregonstate.edu/))
  * [[archive:bioinformatic_tools:ray|Ray]]((http://denovoassembler.sourceforge.net/))
  * [[bioinformatic_tools:solid|SOLiD System Tools (Corona_lite, etc)]]((http://solidsoftwaretools.com/gf/))
  * [[archive:bioinformatic_tools:soapdenovo|SOAPdenovo]]((http://soap.genomics.org.cn/))
  * [[bioinformatic_tools:Shorty|Shorty]]((http://www.cs.sunysb.edu/~skiena/shorty/))
  * [[archive:bioinformatic_tools:price|PRICE]]((http://derisilab.ucsf.edu/software/price/index.html/))
  * [[archive:bioinformatic_tools:sga|Sanger String Graph Assembler]]((http://people.pwf.cam.ac.uk/js779/))
  * [[archive:bioinformatic_tools:pe_assembler|PE-Assembler]]((http://www.comp.nus.edu.sg/~bioinfo/peasm/))



== Probably Proprietary Tools and Services == 
  * [[archive:bioinformatic_tools:clc_genomics_workbench|CLC Bio De-novo Assembler]]((http://www.clcbio.com/index.php?id=1413))
  * [[bioinformatic_tools:codoncode_aligner|CodonCode Aligner]]((http://www.codoncode.com/aligner/))
  * [[archive:bioinformatic_tools:nextgene|NextGENe]]((http://softgenetics.com/NextGENe.html))
  * [[archive:bioinformatic_tools:gs_de_novo_assembler|GS De Novo Assembler (aka Newbler)]]((http://454.com/products-solutions/analysis-tools/gs-de-novo-assembler.asp))
  * [[bioinformatic_tools:sequencher|Sequencher]]((http://www.genecodes.com/))
  * [[bioinformatic_tools:seqman|SeqMan]]((http://www.dnastar.com/t-sub-products-lasergene-seqmanpro.aspx))

=== Mapping tools ===

Tools used to map reads or contigs onto contigs, scaffolds, or genomes.
  * [[bioinformatic_tools:blast|BLAST]] 
  * [[bioinformatic_tools:megablast|Megablast]]
  * [[bioinformatic_tools:blat|Blat]]
  * [[bioinformatic_tools:bowtie|Bowtie]]
  * [[archive:bioinformatic_tools:bwa|BWA]]
  * [[archive:bioinformatic_tools:saruman|SARUMAN]]

=== Data Transfer Tools ===
  * [[archive:bioinformatic_tools:udt|UDT]] ((http://udt.sourceforge.net/)) TCP too slow? Transfer data fast with UDT via UDP.

=== Visualization Tools ===
  * [[bioinformatic_tools:hawkeye|Hawkeye]]((http://sourceforge.net/apps/mediawiki/amos/index.php?title=Hawkeye)) Visualize and validate assemblies.
  * [[bioinformatic_tools:artemis|Artemis]] ((http://www.sanger.ac.uk/resources/software/artemis/)) Visualize and annotate genomic sequences
  * [[bioinformatic_tools:consed|Consed]] ((http://www.phrap.org/consed/consed.html)) Visualize assemblies. Compatible with Newbler output

=== Utilities ===
  * [[archive:bioinformatic_tools:pluck-scripts|pluck-scripts]] Python scripts written by Kevin Karplus.
  * [[computer_resources:rdb|rdb]] Perl scripts for handling tab-separated columns as if they were a relational database.
  * [[computer_resources:sff_extract|sff_extract]] Python script to extra sff files into standard component files (.fasta, .fasta.qual, .xml) (Overlaps in functionality with the Roche-provided sffinfo tool, which may do a better job of decoding flow-space to base space.)
  * [[computer_resources:illuminaToFastq|illuminaToFastq]] C program to convert the illumina .txt files into fastq format, discarding pairs of reads that do not both pass illumina's quality filter.
  * [[archive:bioinformatic_tools:samtools|SAM Tools]] A utility for manipulating alignments in SAM format.
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