Chris:LabNotes/Microbiome/2013/2013-5-14
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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 | V Validation of assembly (using assembly statistics and core genes search) | V Assembly of whole Illumina dataset | V Integration of Moleculo with Illumina reads | V Validation of hybrid assembly (assembly statistics, core genes search, assembly errors)
- A more detailed plan can be found in: File:Moleculo Data Analysis Plan 5 14 2013.docx
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>