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=Moleculo Data Analysis Part 2= *Continued from <http://genome-tech.ucsd.edu/LabNotes/index.php/Chris:LabNotes/Microbiome/2013/2013-5-14#Procedure> ===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 *The steps for correction: (specifically for 1a_Illumina_Test_Assembly_Control) 1) Make config files for pregraph, map, and GapCorrect *Pregraph config file <test_assembly_control.cfg> **Used parameters similar to Assemblathon2 **Key feature is that for both libraries, we are specifying the original read files (q1,q2) instead of the paired corrected file #maximal read length max_rd_len=200 [LIB] name=HB_gDNA200b_121224L1-4_filtered #average insert size avg_ins=200 #if sequence needs to be reversed reverse_seq=0 #in which part(s) the reads are used asm_flags=3 #in which order the reads are used while scaffolding rank=1 # cutoff of pair number for a reliable connection (default 3) pair_num_cutoff=3 q1=/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA200b_121224L1-4_R1_filtered.fastq.gz q2=/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA200b_121224L1-4_R2_filtered.fastq.gz [LIB] name=HB_gDNA2kb_NoIndex_L005_001_filtered avg_ins=2000 reverse_seq=1 asm_flags=2 rank=2 pair_num_cutoff=5 map_len=35 q1=/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA2kb_NoIndex_L005_R1_001_filtered.fastq.gz q2=/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA2kb_NoIndex_L005_R2_001_filtered.fastq.gz *Map config file <test_assembly_control.map.cfg> **Same as the pregraph config file, just without the max read length parameter [LIB] name=HB_gDNA200b_121224L1-4_filtered #average insert size avg_ins=200 #if sequence needs to be reversed reverse_seq=0 #in which part(s) the reads are used asm_flags=3 #in which order the reads are used while scaffolding rank=1 # cutoff of pair number for a reliable connection (default 3) pair_num_cutoff=3 q1=/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA200b_121224L1-4_R1_filtered.fastq.gz q2=/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA200b_121224L1-4_R2_filtered.fastq.gz [LIB] name=HB_gDNA2kb_NoIndex_L005_001_filtered avg_ins=2000 reverse_seq=1 asm_flags=2 rank=2 pair_num_cutoff=5 map_len=35 q1=/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA2kb_NoIndex_L005_R1_001_filtered.fastq.gz q2=/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA2kb_NoIndex_L005_R2_001_filtered.fastq.gz *Gap Closer config file <test_assembly_control.GC.cfg> **Only need to include library for 200bp reads (no need for scaffolding reads) [LIB] name=HB_gDNA200b_121224L1-4_filtered #average insert size avg_ins=200 #if sequence needs to be reversed reverse_seq=0 #in which part(s) the reads are used asm_flags=3 #in which order the reads are used while scaffolding rank=1 # cutoff of pair number for a reliable connection (default 3) pair_num_cutoff=3 q1=/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA200b_121224L1-4_R1_filtered.fastq.gz q2=/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA200b_121224L1-4_R2_filtered.fastq.gz 2) Write commands for assembly (ass.sh) *Here, we are writing commands for assembly in separate command lines (in order to better control each part of assembly) **Need commands for pregraph, contig, map, and scaff /home/cjwei/software/SOAPdenovo2-src-r223/standardPregraph/SOAPdenovo-63mer pregraph -s /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/test_assembly_control.cfg -d 1 -p 32 -K 29 -o /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/test_assembly_control >/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/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_2013/1a_Illumina_Test_Assembly_Control/test_assembly_control -M 3 >/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/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_2013/1a_Illumina_Test_Assembly_Control/test_assembly_control.map.cfg -g /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/test_assembly_control -p 32 >/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/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_2013/1a_Illumina_Test_Assembly_Control/test_assembly_control -b 1.2 -F -p 32 > /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/scaff.log 3) Write command for GapCloser <GapCloser.sh> *This is performed after assembly and scaffolding /home/cjwei/software/SOAPdenovo2-src-r223/tools/GapCloser -a /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/test_assembly_control.scafSeq -b /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/test_assembly_control.GC.cfg -l 200 -o /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/test_assembly_control.scafSeq.GC -p 29 -t 32 >/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/GapCloser.log 4) Create 1a_control_assembly in order to submit for Triton to run *'''The steps for assembly for using corrected 200bp and/or corrected 2kb reads were modified to switch q1,q2 to p in the config files in order to switch to corrected files'''
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