Chris:LabNotes/Moleculo/2013/2013-5-28
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Slide Shortening Illumina+Moleculo Hybrid Assembly Test[edit]
Background[edit]
- Dr. Zhang suggested to use slide shortening procedure to improve hybrid assembly with Illumina scaffolds + Moleculo reads (because there is probably very little overlap between Illumina scaffolds, especially long scaffolds)
- Previously, I performed slide shortening on SAG+metagenomic hybrid assembly on <http://genome-tech.ucsd.edu/LabNotes/index.php/Chris:LabNotes/Microbiome/2011/2011-5-2> <http://genome-tech.ucsd.edu/LabNotes/index.php/Chris:LabNotes/Microbiome/2011/2011-6-3> and found that assembly improved when cutting >2000bp contigs+100bp sliding window
- We want to improve on the Illumina+Moleculo hybrid assembly from <http://genome-tech.ucsd.edu/LabNotes/index.php/Chris:LabNotes/Microbiome/2013/2013-5-17>
- Here, I'll be testing which slide shortening protocol to use and optimizing various parameters
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
- Will slide shortening on Illumina help with assembly?
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>