Chris:LabNotes/Moleculo/2013/2013-5-21
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Illumina + Moleculo Assembly (on all reads)[edit]
- Continued from <http://genome-tech.ucsd.edu/LabNotes/index.php/Chris:LabNotes/Microbiome/2013/2013-5-17>
Background[edit]
- Previously, we were able to run Test Assembly + Moleculo hybrid assembly
- Now, we want to perform hybrid assembly using all the data that we have
Procedure[edit]
Illumina Read Correction[edit]
- Illumina read correction was performed similar to previously using kmerfreq and correct_error scripts
- Correction scripts found in Triton </projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/3a_Illumina_All_correction>
- Correction reads found in Triton </projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw>
- Results from correction are summarized in File:5 21 2013 Assembly read stats.xlsx
Illumina Assembly[edit]
- Assembly was performed on all of the Illumina data using SOAPdenovo
- Assembly found in Triton </projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/3b_Illumina_All_assembly>
- Used similar configuration/parameters as test assembly, but added all reads
/home/cjwei/software/SOAPdenovo2-src-r223/standardPregraph/SOAPdenovo-63mer pregraph -s /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/3b_Illumina_All_assembly/Illumina_all_assembly.cfg -d 1 -p 32 -K 29 -o /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/3b_Illumina_All_assembly/Illumina_all_assembly >/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/3b_Illumina_All_assembly/pregraph.log
/home/cjwei/software/SOAPdenovo2-src-r223/standardPregraph/SOAPdenovo-63mer contig -g /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/3b_Illumina_All_assembly/Illumina_all_assembly -M 3 >/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/3b_Illumina_All_assembly/contig.log
/home/cjwei/software/SOAPdenovo2-src-r223/standardPregraph/SOAPdenovo-63mer map -s /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/3b_Illumina_All_assembly/Illumina_all_assembly.map.cfg -g /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/3b_Illumina_All_assembly/Illumina_all_assembly -p 32 >/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/3b_Illumina_All_assembly/map.log
/home/cjwei/software/SOAPdenovo2-src-r223/standardPregraph/SOAPdenovo-63mer scaff -g /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/3b_Illumina_All_assembly/Illumina_all_assembly -b 1.2 -F -p 32 >/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/3b_Illumina_All_assembly/scaff.log
- GapCloser run
/home/cjwei/software/SOAPdenovo2-src-r223/tools/GapCloser -a /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/3b_Illumina_All_assembly/Illumina_all_assembly.scafSeq -b /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/3b_Illumina_All_assembly/Illumina_all_assembly.GC.cfg -l 200 -o /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/3b_Illumina_All_assembly/Illumina_all_assembly.scafSeq.GC -p 29 -t 32 >/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/3b_Illumina_All_assembly/GapCloser.log