D03-NextGen-Bio-NGS
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D03-NextGen-Bio-NGS D03-NextGen-Bio-NGS Presentation Transcript

  • Bio-­‐NGS:  BioRuby  plugin  to  conduct   programmable  workflows  for     Next  Genera?on  Sequencing  data   Raoul  J.P.  Bonnal   co-­‐authors   bonnal@ingm.org   Francesco  Strozzi   Valeria  Ranzani   Integra(ve  Biology  Program   Toshiaki  Katayama   Is(tuto  Nazionale  di  Gene(ca  Molecolare   Italy  July  15,  2011   BOSC,  Vienna,  Austria  
  • Bio-­‐Gem   authors:  Raoul  J.P.  Bonnal,  Pjotr  Prins,  Toshiaki  Katayama  •  a  soOware  generator  for  crea(ng  BioRuby   plugins  •  last  year  (@BOSC  2010)  was  an  idea  and  a  prototype  •  Features:   • bio-­‐assembly  (0.1.0)   • bio-­‐isoelectric_point  (0.1.1)   • bio-­‐blastxmlparser  (0.6.1)   • bio-­‐kb-­‐illumina  (0.1.0)   • bio-­‐bwa  (0.2.2)   • bio-­‐lazyblastxml  (0.4.0)   –  Extend  BioRuby   • bio-­‐cnls_screenscraper   (0.1.0)   • bio-­‐ • bio-­‐logger  (0.9.0)   • bio-­‐nexml  (0.0.1)   • bio-­‐ngs  (0.2.1)   –  Modularity   emboss_six_frame_nucleo(de • bio-­‐octopus  (0.1.1)   _sequences  (0.1.0)   • bio-­‐gem  (0.2.2)   • bio-­‐samtools  (0.2.4)   • bio-­‐sge  (0.0.0)   –  Easy   • bio-­‐genomic-­‐interval  (0.1.2)   • bio-­‐tm_hmm  (0.2.0)   • bio-­‐gff3  (0.8.6)   • bio-­‐graphics  (1.4)   • bio-­‐ucsc-­‐api  (0.1.0)   •  sharing:packaging:publishing   • bio-­‐hello  (0.0.0)   –  Just  Code  !   Dev:  hcps://github.com/helios/bioruby-­‐gem   Install:  gems  install  bio-­‐gem  July  15,  2011   BOSC,  Vienna,  Austria  
  • Bio-­‐NGS   An  Applica(on   A  SoOware  Development  Framework   A  Project  Environment  July  15,  2011   BOSC,  Vienna,  Austria  
  • Applica(on  •  Stand  alone   –  Auto  install  everything  it  needs  –  sandbox/isola*on-­‐   –  System-­‐wide  or  User  (RVM  –Ruby  Version  Manager-­‐)  •  Mul(  plagorms   –  Linux,  OS  X   –  MRI,  JRuby  •  Command  line   –  Thor:  a  simple  and  efficient  tool  for  building  self-­‐documen(ng  command   line  u(li(es  •  Common  syntax  to  different  applica(ons  •  Collec(on  of  Tasks   –  Basic,  Advanced   RVM  hcps://rvm.beginrescueend.com/   Thor  hcps://github.com/wycats/thor    July  15,  2011   BOSC,  Vienna,  Austria  
  • SoOware  Development  Framework  •  Expand  BioRuby’s  func(onali(es  to  NGS   •  API  +  Consistent  Namespace  •  Integrate  third-­‐party  tools   •  Wrapping  :  quick,  easy  support,  increase  produc(vity   •  Binding  :  low-­‐level  func(onali(es  •  Modular,  reuse  other  plug-­‐ins   •  BioBwa  (binding)   •  BioSamtools  (binding)  July  15,  2011   BOSC,  Vienna,  Austria  
  • Project  Environment  •  Directory  scaffold  •  Customize   –  Tasks  :  Thor  or  Rake  (Ruby  DSL)     –  Configura(ons:  YAML  •  History  •  Embedded  DB   –  SQLite3  July  15,  2011   BOSC,  Vienna,  Austria  
  • Tools   e/ Bow(   BWA ?   ?   More…   Quant   FASTX-­‐ Toolkit  July  15,  2011   BOSC,  Vienna,  Austria  
  • Tools   Bio-­‐NGS   Primary:     Secondary:   Ter(ary:   Pre-­‐Processing   Alignment   Knowledge   Conversion,  Filter,     Bow(e/ TopHat   Samtools   Cufflinks   Ontology   FASTX-­‐Toolkit   BWA   More…   BAM   More…   Differen(al   More…  Illumina  bcl   FASTQ   Quant   Expression   Local   Execu(on   Distributed/Parallel   July  15,  2011   BOSC,  Vienna,  Austria  
  • Wrapper  module Bio module Ngs module Cufflinks class Compare include Bio::Command::Wrapper set_program Bio::Ngs::Utils.binary("cufflinks/cuffcompare") use_aliases add_option "outprefix", :type => :string, :aliases => -o, :default => "Comparison" add_option "gtf_combine_file", :type => :string, :aliases => -i add_option "gtf_reference", :type => :string, :aliases => -r add_option "only_overlap", :type => :boolean, :aliases => -R add_option "discard_transfrags", :type => :boolean, :aliases => -M’ end end endendJuly  15,  2011   BOSC,  Vienna,  Austria  
  • Wrapper  module Bio module Ngs module Cufflinks class Compare include Bio::Command::Wrapper set_program Bio::Ngs::Utils.binary("cufflinks/cuffcompare") use_aliases add_option "outprefix", :type => :string, :aliases => -o, :default => "Comparison" add_option "gtf_combine_file", :type => :string, :aliases => -i add_option "gtf_reference", :type => :string, :aliases => -r irb(main):001:0> require:type => :boolean, :aliases => -R add_option "only_overlap", ‘bio-ngs’ add_option "discard_transfrags", :type => :boolean, :aliases => -M’ irb(main):001:1> cuffcompare = Bio::Ngs::Cufflinks::Compare.new irb(main):001:2> cuffcompare.params = {….} irb(main):001:3> cuffcompare.run(:arguments=>[…]) end end => #<Bio::Ngs::Cufflinks::Compare:0x0000000c1630f8 @program="/ endend usr/local/lib/ruby/gems/1.9.1/gems/bio-ngs-0.2.1/lib/bio/ngs/ ext/bin/linux/cufflinks/cuffcompare", @options={}, @params={}>July  15,  2011   BOSC,  Vienna,  Austria  
  • Tasks  No  binary  found  with  this  name:  setupBclToQseq.py   biongs  convert:qseq:fastq:samples_by_lane  SAMPLES  LANE   project  No  binary  found  with  this  name:  fastq_quality_boxplot_graph.sh   OUTPUT   -­‐-­‐-­‐-­‐-­‐-­‐-­‐  No  binary  found  with  this  name:  blastn   biongs  project:new  [NAME]    No  binary  found  with  this  name:  blastx   history   biongs  project:update  [TYPE]  WARNING:  no  program  is  associated  with  BCLQSEQ  task,  does   -­‐-­‐-­‐-­‐-­‐-­‐-­‐   not  make  sense  to  create  a  thor  task.   biongs  history:8            #  Task  convert:illumina:de:isoform   quality  WARNING:  no  program  is  associated  with  BLASTN  task,  does  not   PARAMETERS:  /Users/bonnalraoul/Desktop/ make  sense  to  create  a  thor  task.   RRep16giugno/DE_lane1-­‐2-­‐3-­‐4-­‐6-­‐8/DE_lane1-­‐2-­‐3-­‐4-­‐6-­‐8/ -­‐-­‐-­‐-­‐-­‐-­‐-­‐   isoform_exp.diff  /Users/bonnalraoul/Desktop/ biongs  quality:boxplot  FASTQ_QUALITY_STATS  WARNING:  no  program  is  associated  with  BLASTX  task,  does  not   RRep16giugno/COMPARE_lane1-­‐2-­‐3-­‐4-­‐6-­‐8/COMPA...   biongs  quality:fastq_stats  FASTQ    make  sense  to  create  a  thor  task.   biongs  quality:illumina_b_profile_raw  FASTQ  -­‐-­‐read-­‐length=N  bwa   homology   biongs  quality:illumina_b_profile_svg  FASTQ  -­‐-­‐read-­‐length=N    -­‐-­‐-­‐   -­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐   biongs  quality:reads  FASTQ  biongs  bwa:aln:long  [FASTQ]  -­‐-­‐file-­‐out=FILE_OUT  -­‐-­‐prefix=PREFIX  biongs  homology:convert:blast2text  [XML  FILE]  -­‐-­‐file-­‐ biongs  quality:reads_coverage  FASTQ_QUALITY_STATS  biongs  bwa:aln:short  [FASTQ]  -­‐-­‐file-­‐out=FILE_OUT  -­‐-­‐ out=FILE_OUT   biongs  quality:scacerplot  EXPR1  EXPR2  OUTPUT   prefix=PREFIX   biongs  homology:convert:go2json   biongs  quality:trim  FASTQ                                                                          biongs  bwa:index:long  [FASTA]  biongs  bwa:index:short  [FASTA]   biongs  homology:db:export  [TABLE]  -­‐-­‐fileout=FILEOUT   rna  biongs  bwa:sam:paired  -­‐-­‐fastq=one  two  three  -­‐-­‐file-­‐ biongs  homology:db:init   out=FILE_OUT  -­‐-­‐prefix=PREFIX  -­‐-­‐sai=one  two  three     -­‐-­‐-­‐   biongs  bwa:sam:single  [SAI]  -­‐-­‐fastq=FASTQ  -­‐-­‐file-­‐ biongs  homology:download:all   biongs  rna:compare  GTF_REF  OUTPUTDIR   out=FILE_OUT  -­‐-­‐prefix=PREFIX   biongs  homology:download:goannota(on     GTFS_QUANTIFICATION   biongs  homology:download:uniprot   biongs  rna:idx2fasta  INDEX  FASTA  convert   biongs  homology:load:blast  [FILE]   biongs  rna:mapquant  DIST  INDEX  OUTPUTDIR  FASTQS  -­‐-­‐-­‐-­‐-­‐-­‐-­‐   biongs  homology:load:goa   biongs  rna:quant  GTF  OUTPUTDIR  BAM  biongs  convert:bam:extract_genes  BAM  GENES  -­‐-­‐ensembl-­‐ biongs  homology:report:blast   biongs  rna:tophat  DIST  INDEX  OUTPUTDIR  FASTQS   release=N  -­‐o,  -­‐-­‐output=OUTPUT  biongs  convert:bam:merge  -­‐i,  -­‐-­‐input-­‐bams=one  two  three   ontology   sff  biongs  convert:bam:sort  BAM  [PREFIX]   -­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐   -­‐-­‐-­‐  biongs  convert:bcl:qseq:convert  RUN  OUTPUT  [JOBS]     biongs  ontology:db:export  [TABLE]  -­‐-­‐fileout=FILEOUT   biongs  sff:extract  [FILE]  biongs  convert:illumina:de:gene  DIFF  GTF   biongs  ontology:db:init  biongs  convert:illumina:de:isoform  DIFF  GTF   biongs  ontology:download:all  biongs  convert:illumina:de:rename_qs  DIFF_FILE  NAMES   biongs  ontology:download:go  biongs  convert:illumina:fastq:trim_b  FASTQ   biongs  ontology:download:goslim  biongs  convert:illumina:humanize:build_compare_kb  GTF   biongs  ontology:load:genego  [FILE]  biongs  convert:illumina:humanize:isoform_exp  GTF  ISOFORM   biongs  ontology:load:go  [FILE]  biongs  convert:qseq:fastq:by_file  FIRST  OUTPUT   biongs  ontology:report:go  biongs  convert:qseq:fastq:by_lane  LANE  OUTPUT  biongs  convert:qseq:fastq:by_lane_index  LANE  INDEX  OUTPUT  July  15,  2011   BOSC,  Vienna,  Austria  
  • N o   B i n a r y   Tasks   Task   disabled  No  binary  found  with  this  name:  setupBclToQseq.py   biongs  convert:qseq:fastq:samples_by_lane  SAMPLES  LANE   project   Keep   OUTPUT  No  binary  found  with  this  name:  fastq_quality_boxplot_graph.sh  No  binary  found  with  this  name:  blastn   -­‐-­‐-­‐-­‐-­‐-­‐-­‐   biongs  project:new  [NAME]     everything  No  binary  found  with  this  name:  blastx   history   biongs  project:update  [TYPE]  WARNING:  no  program  is  associated  with  BCLQSEQ  task,  does   -­‐-­‐-­‐-­‐-­‐-­‐-­‐   not  make  sense  to  create  a  thor  task.   biongs  history:8            #  Task  convert:illumina:de:isoform   organized   quality  WARNING:  no  program  is  associated  with  BLASTN  task,  does  not   PARAMETERS:  /Users/bonnalraoul/Desktop/ make  sense  to  create  a  thor  task.   RRep16giugno/DE_lane1-­‐2-­‐3-­‐4-­‐6-­‐8/DE_lane1-­‐2-­‐3-­‐4-­‐6-­‐8/ -­‐-­‐-­‐-­‐-­‐-­‐-­‐   isoform_exp.diff  /Users/bonnalraoul/Desktop/ biongs  quality:boxplot  FASTQ_QUALITY_STATS  WARNING:  no  program  is  associated  with  BLASTX  task,  does  not   RRep16giugno/COMPARE_lane1-­‐2-­‐3-­‐4-­‐6-­‐8/COMPA...   biongs  quality:fastq_stats  FASTQ    make  sense  to  create  a  thor  task.   biongs  quality:illumina_b_profile_raw  FASTQ  -­‐-­‐read-­‐length=N  bwa   homology   biongs  quality:illumina_b_profile_svg  FASTQ  -­‐-­‐read-­‐length=N    -­‐-­‐-­‐   -­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐   biongs  quality:reads  FASTQ  biongs  bwa:aln:long  [FASTQ]  -­‐-­‐file-­‐out=FILE_OUT  -­‐-­‐prefix=PREFIX  biongs  homology:convert:blast2text  [XML  FILE]  -­‐-­‐file-­‐ biongs  quality:reads_coverage  FASTQ_QUALITY_STATS  biongs  bwa:aln:short  [FASTQ]  -­‐-­‐file-­‐out=FILE_OUT  -­‐-­‐ out=FILE_OUT   biongs  quality:scacerplot  EXPR1  EXPR2  OUTPUT   prefix=PREFIX  biongs  bwa:index:long  [FASTA]   biongs  homology:convert:go2json   Repor(ng   biongs  quality:trim  FASTQ                                                                          biongs  bwa:index:short  [FASTA]  biongs  bwa:sam:paired  -­‐-­‐fastq=one  two  three  -­‐-­‐file-­‐ Recall  an   biongs  homology:db:export  [TABLE]  -­‐-­‐fileout=FILEOUT   rna   biongs  homology:db:init   -­‐-­‐-­‐   old   out=FILE_OUT  -­‐-­‐prefix=PREFIX  -­‐-­‐sai=one  two  three     biongs  bwa:sam:single  [SAI]  -­‐-­‐fastq=FASTQ  -­‐-­‐file-­‐ out=FILE_OUT  -­‐-­‐prefix=PREFIX   biongs  homology:download:all   biongs  homology:download:goannota(on     biongs  rna:compare  GTF_REF  OUTPUTDIR   GTFS_QUANTIFICATION  convert   analysis   biongs  homology:download:uniprot   biongs  homology:load:blast  [FILE]   biongs  rna:idx2fasta  INDEX  FASTA   biongs  rna:mapquant  DIST  INDEX  OUTPUTDIR  FASTQS  -­‐-­‐-­‐-­‐-­‐-­‐-­‐   biongs  homology:load:goa   biongs  rna:quant  GTF  OUTPUTDIR  BAM  biongs  convert:bam:extract_genes  BAM  GENES  -­‐-­‐ensembl-­‐ biongs  homology:report:blast   biongs  rna:tophat  DIST  INDEX  OUTPUTDIR  FASTQS   release=N  -­‐o,  -­‐-­‐output=OUTPUT  biongs  convert:bam:merge  -­‐i,  -­‐-­‐input-­‐bams=one  two  three   ontology   sff  biongs  convert:bam:sort  BAM  [PREFIX]   -­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐   -­‐-­‐-­‐  biongs  convert:bcl:qseq:convert  RUN  OUTPUT  [JOBS]     biongs  ontology:db:export  [TABLE]  -­‐-­‐fileout=FILEOUT   biongs  sff:extract  [FILE]  biongs  convert:illumina:de:gene  DIFF  GTF   biongs  ontology:db:init  biongs  convert:illumina:de:isoform  DIFF  GTF   biongs  ontology:download:all  biongs  convert:illumina:de:rename_qs  DIFF_FILE  NAMES   biongs  ontology:download:go  biongs  convert:illumina:fastq:trim_b  FASTQ   biongs  ontology:download:goslim  biongs  convert:illumina:humanize:build_compare_kb  GTF   biongs  ontology:load:genego  [FILE]  biongs  convert:illumina:humanize:isoform_exp  GTF  ISOFORM   biongs  ontology:load:go  [FILE]  biongs  convert:qseq:fastq:by_file  FIRST  OUTPUT  biongs  convert:qseq:fastq:by_lane  LANE  OUTPUT   biongs  ontology:report:go   Basic   Advanced  biongs  convert:qseq:fastq:by_lane_index  LANE  INDEX  OUTPUT  July  15,  2011   BOSC,  Vienna,  Austria  
  • Tasks   class Rna < Thor desc "mapquant DIST INDEX OUTPUTDIR FASTQS", "map and quantify" method_option :paired, :type => :boolean, :default => false, :desc => Are reads paired? If you chose this option pass just the basename of the file without forward/reverse and .fastq def mapquant(dist, index, outputdir, fastqs) #tophat invoke :tophat, [dist, index, outputdir, fastqs], :paired=>options.paired #cufflinks quantification on gtf invoke :quant, ["#{index}.gtf", File.join(outputdir,"quantification"), File.join(outputdir,"accepted_hits_sort.bam")] end … endJuly  15,  2011   BOSC,  Vienna,  Austria  
  • Tasks   class Rna < Thor # youll end up with 3 accept file, regular, sorted, sorted-indexed desc "tophat DIST INDEX OUTPUTDIR FASTQS", "run tophat as from command line, default 6 processors and then create a sorted bam indexed." method_option :paired, :type => :boolean, :default => false, :desc => Are reads paired? If you chose this option pass just the…’ Bio::Ngs::Tophat.new.thor_task(self, :tophat) do |wrapper, task, dist, index, outputdir, fastqs| wrapper.params = task.options #merge passed options to the wrapper. wrapper.params = {"mate-inner-dist"=>dist, "output-dir"=>outputdir, "num-threads"=>6, "solexa1.3-quals"=>true} fastq_files = task.options[:paired] ? ["#{fastqs}_forward.fastq","#{fastqs}_reverse.fastq"] : ["#{fastqs}"] wrapper.run :arguments=>[index, fastq_files ].flatten, :separator=>"=" class Rna < Thor accepted_hits_bam_fn = File.join(outputdir, "accepted_hits.bam") desc "mapquant DIST INDEX OUTPUTDIR FASTQS", "map and quantify" method_option :paired, "convert:bam:sort", :default => false, :desc => Are reads paired? If you chose task.invoke :type => :boolean, [accepted_hits_bam_fn] # call the sorting procedure. end this option pass just the basename end of the file without forward/reverse and .fastq def mapquant(dist, index, outputdir, fastqs) #tophat invoke :tophat, [dist, index, outputdir, fastqs], :paired=>options.paired #cufflinks quantification on gtf invoke :quant, ["#{index}.gtf", File.join(outputdir,"quantification"), File.join(outputdir,"accepted_hits_sort.bam")] end … endJuly  15,  2011   BOSC,  Vienna,  Austria  
  • Tasks   class Rna < Thor # youll end up with 3 accept file, regular, sorted, sorted-indexed desc "tophat DIST INDEX OUTPUTDIR FASTQS", "run tophat as from command line, default 6 processors and then create a sorted bam indexed." method_option :paired, :type => :boolean, :default => false, :desc => Are reads paired? If you chose this option pass just the…’ Bio::Ngs::Tophat.new.thor_task(self, :tophat) do |wrapper, task, dist, index, outputdir, fastqs| wrapper.params = task.options #merge passed options to the wrapper. wrapper.params = {"mate-inner-dist"=>dist, "output-dir"=>outputdir, "num-threads"=>6, "solexa1.3-quals"=>true} fastq_files = task.options[:paired] ? ["#{fastqs}_forward.fastq","#{fastqs}_reverse.fastq"] : ["#{fastqs}"] wrapper.run :arguments=>[index, fastq_files ].flatten, :separator=>"=" class Rna < Thor accepted_hits_bam_fn = File.join(outputdir, "accepted_hits.bam") desc "mapquant DIST INDEX OUTPUTDIR FASTQS", "map and quantify" method_option :paired, "convert:bam:sort", :default => false, :desc => Are reads paired? If you chose task.invoke :type => :boolean, [accepted_hits_bam_fn] # call the sorting procedure. end this option pass just the basename end of the file without forward/reverse and .fastq def mapquant(dist, index, outputdir, fastqs) #tophat invoke :tophat, [dist, index, outputdir, fastqs], :paired=>options.paired #cufflinks quantification on gtf invoke :quant, ["#{index}.gtf", File.join(outputdir,"quantification"), File.join(outputdir,"accepted_hits_sort.bam")] end … end class Rna < Thor desc "quant GTF OUTPUTDIR BAM ", "Genes and transcripts quantification" Bio::Ngs::Cufflinks::Quantification.new.thor_task(self, :quant) do |wrapper, task, gtf, outputdir, bam| wrapper.params = task.options wrapper.params = {"num-threads" => 6, "output-dir" => outputdir, "GTF" => gtf } wrapper.run :arguments=>[bam], :separator => "=" end endJuly  15,  2011   BOSC,  Vienna,  Austria  
  • Next?  •  Support  more  soOware,  not  only  NGS   •  Wrap  EMBOSS  on  the  fly  reading  acd  files  •  Tune  according  to  hardware  •  Share  tasks   –  Thor  &  Rake  •  Improve  JRuby  compa(bility    •  Contributes  •  Scalability   –  Cloud  ?  BioLinux   –  BioHub:  distribute  tasks  using  messaging   •  Ac(veMQ   •  Stomp   •  Ac(veMessaging   •  Adapters  for  Queuing  Systems  July  15,  2011   BOSC,  Vienna,  Austria  
  • Next?  •  Support  more  soOware,  not  only  NGS   •  Wrap  EMBOSS  on  the  fly  reading  acd  files  •  Tune  according  to  hardware  •  Share  tasks   –  Thor  &  Rake  •  Improve  JRuby  compa(bility    •  Contributes  •  Scalability   –  Cloud  ?  BioLinux   –  BioHub:  distribute  tasks  using  messaging   •  Ac(veMQ   •  Stomp   •  Ac(veMessaging   •  Adapters  for  Queuing  Systems  July  15,  2011   BOSC,  Vienna,  Austria  
  • Acknowledgments   Serena  Cur(   Francesco  Strozzi1,3   Groningen  Bioinforma(cs  Centre   Debora  Mascheroni   Pjotr  Prins2   Alessandra  Stella   Valeria  Parente   Valeria  Ranzani1   Anna  Ripamon(   Grazisa  Rossez   Riccardo  L.  Rossi    Laboratory  of  Genome  Database   Dan  MacLean  4   Roberto  Sciarreca   Toshiaki  Katayama1,2   The  Genome  Analysis  Centre   Ricardo  Ramirez-­‐Gonzalez  4   Massimiliano  Pagani  1  bio-­‐ngs,  2  bio-­‐gem,  3  bio-­‐bwa,  4  bio-­‐samtools  July  15,  2011   BOSC,  Vienna,  Austria  
  • Ques(ons  ?   INFO   E-­‐mail:  bonnal@ingm.org  /  r@bioruby.org     Dev      :  hcp://github/helios/bioruby-­‐ngs     Docs  :  hcps://github.com/helios/bioruby-­‐ngs/blob/master/README.rdoc       Wiki    :  hcp://bioruby.open-­‐bio.org/wiki/Next_Genera(on_Sequencing     BioRuby-­‐ML:  hcp://lists.open-­‐bio.org/mailman/lis(nfo/bioruby     Irc:  #bioruby  (  irc.freenode.org  )  July  15,  2011   BOSC,  Vienna,  Austria