Chris:LabNotes/Moleculo/2013/2013-5-28

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Slide Shortening Illumina+Moleculo Hybrid Assembly Test[edit]

Background[edit]

Plan[edit]

  • Will be working with the smaller test assembly that was previously performed using SOAPdenovo on select libraries:
HB_gDNA200b_121224L1-4_R*_filtered
HB_gDNA2kb_NoIndex_L005_R*_001_filtered
  • Proposed test assembly conditions:
    • Slide shortening (>2000bp, slide 100bp, copy number 3) on Illumina scaffolds + Celera assembly with Moleculo
    • Slide shortening (>2000bp, slide 100bp, copy number 3) on Illumina scaffolds + SOAPdenovo assembly with Moleculo
    • Note: For all tests, also include a copy of the original scaffolds/reads prior to slide shortening in order to retain long sequence advantage
  • These conditions tested will answer the following questions:
    • Will slide shortening on Illumina help with assembly?
      • May prevent discarding Illumina scaffolds due to minimum cutoff parameters
    • Will SOAPdenovo be a better assembler than Celera if the input sequences are shortened?
      • Koren's paper suggested that overlap consensus assembly was the preferred method for assembling single contigs assembled from long sequences

Procedure[edit]

  • Slide shortening test found in my genemapster </media/disk-2/cjwei/130419_Oncomelania_Illumina_Moleculo/Triton_Hybrid_Assembly_5_13_2013/1c_Illumina_Test_Assembly+Moleculo_sliding-cut_test> and Triton </projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1c_Illumina_Test_Assembly_all-correction_sliding-cut_test/SOAPdenovo_slide-shortening>