Chris:LabNotes/Microbiome/2013/2013-5-15

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Revision as of 19:07, 15 May 2013 by >Cjwei
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Moleculo Data Analysis Part 2

1a-c_Illumina_Test_Assembly

  • Triton folder: </projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/>
  • We are going to now run SOAPdenovo2 assembly on corrected read files
  • In order to do this, we are going to test three different conditions for assembly (each found in their consecutive folders):
    • <1a_Illumina_Test_Assembly_Control>: Assembly using only non-corrected original reads
    • <1b_Illumina_Test_Assembly_no-Mate-correction>: Assembly using corrected 200bp reads with no correction on mate-paired 2kb reads (this is the protocol used in Assemblathon2 in which the reads used to scaffold are not corrected)
    • <1c_Illumina_Test_Assembly_all-correction>: Assembly using only corrected reads for both 200bp and 2kb mate-paired read files