Chris:LabNotes/Microbiome/2013/2013-5-14

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Revision as of 18:38, 15 May 2013 by >Cjwei
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Moleculo Data Analysis Part 1

Background

  • We are integrating Illumina (short read) and Moleculo (long read) data to assemble the oncomelania genome
  • The overall plan that we are using is:
Test assembly of small Illumina dataset
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         V
Validation of assembly (using assembly statistics and core genes search)
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         V
Assembly of whole Illumina dataset
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         V
Integration of Moleculo with Illumina reads
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         V
Validation of hybrid assembly (assembly statistics, core genes search, assembly errors)

Procedure

0_Illumina_Test_correction

  • Triton Folder: </projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/0_Illumina_Test_correction/>
  • In order to first start with the test assembly of small Illumina dataset, we first want to perform correction of reads and test whether correction will help improve assembly
  • We are using the correction software used in Assemblathon2 by SOAPdenovo: (found in </home/cjwei/software/SOAPdenovo2-src-r223/SOAPdenovoPipeline4BirdInAssemblathon2/>
    • kmerfreq
    • correct_error
  • Steps for error correction:

1)Create read list for correction <reads2cor.lst>, which is just the file location of reads. If have paired read files, must put each file consecutively.

/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA200b_121224L1-4_R1_filtered.fastq.gz
/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA200b_121224L1-4_R2_filtered.fastq.gz
/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA2kb_NoIndex_L005_R1_001_filtered.fastq.gz
/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA2kb_NoIndex_L005_R2_001_filtered.fastq.gz

2) Run commands (need to run kmerfreq then correct_error scripts in order) <1_correction>