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= Data =
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== Short reads ==
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Paired reads are available at [http://www.illumina.com/systems/miseq/scientific_data.ilmn Illumina Miseq] ([ftp://webdata:webdata@ussd-ftp.illumina.com/Data/SequencingRuns/MG1655/MiSeq_Ecoli_MG1655_110721_PF_R1.fastq.gz Mate1], [ftp://webdata:webdata@ussd-ftp.illumina.com/Data/SequencingRuns/MG1655/MiSeq_Ecoli_MG1655_110721_PF_R2.fastq.gz Mate2])
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Read length: 151bp
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Read amount: 5,729,470 X2
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Insert size ~ 300bp
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We converted the required format using Picard tools ([http://picard.sourceforge.net/command-line-overview.shtml ref]).
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java -jar SamToFastq.jar INPUT=Ecoli_MG1655_s_6_1_bfast.bam FASTQ=Ecoli_MG1655_s1.fastq
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java -jar SamToFastq.jar INPUT=Ecoli_MG1655_s_6_2_bfast.bam FASTQ=Ecoli_MG1655_s2.fastq
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We combined MiSeq_Ecoli_MG1655_110721_PF_R1.fastq and MiSeq_Ecoli_MG1655_110721_PF_R2.fastq to MiSeq_PE.fastq.
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java convertFastqToFastaAndQual MiSeq_PE.fastq MiSeq_PE.fna MiSeq_PE.qual
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convert-fasta-to-v2.pl -mean 214 -stddev 21 -m Mate_info -l Illumia_Ecoli -s Ecoli_MG1655_PE.fna -q Ecoli_MG1655_PE.qual > Ecoli_MG1655_PE.frg
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== Long reads ==
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1 SMRT Cell of 10 kbp continuous long reads (CLR) for Escherichia coli K12 MG1655 were downloaded from [https://github.com/PacificBiosciences/DevNet/wiki/E%20coli%20K12%20MG1655%20Hybrid%20Assembly this link].
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The file of PacBio_10kb_CLR.fastq contains ~21X of E. coli CLR reads from a 10kb library that was filtered using standard PacBio filtering thresholds (minimum RQ=0.75, RL=50bp) ([http://files.pacb.com/datasets/secondary-analysis/e-coli-k12-de-novo/1.3.0/README.txt ref]).
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= Assemblies with short reads only =
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Abyss, Edena, SPAdes, SOAPdenovo2, Velvet, CISA (Note at: 20130807_MG1655_s1s2_with_verious_Assemblers)
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MaSuRCA (note at: MaSuRCA assembler)
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= PacBio corrected reads (PBcR) =
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To correct the PacBio CLR with raw short reads:
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pacBioToCA -length 1000 -partitions 200 -l PacBio_Illumia -s pacbio.spec -fastq PacBio_10kb_CLR.fastq Ecoli_MG1655_PE.frg 1>PacBio_Illumia_Ecoli.out 2>error.out
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To correct the PacBio CLR with 100X high-quality reads (p<0.05, length of paired-end read>=100bp)
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pacBioToCA -length 500 -partitions 200 -l PacBio_Illumia -s pacbio.spec -fastq PacBio_10kb_CLR.fastq 100X_Ecoli_PE.frg
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= Assemblies with hybrid methods =
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== Assemble corrected long reads ==
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runCA (20130807_MG1655_s1s2_with_verious_Assemblers for 100X, 20120628_20120628_PacBio_With_CA(Celera Assembler)_Wgs), MIRA3
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== Hybrid assemble from pre-assembled contigs and long reads ==
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AHA, PBJelly, Cerulean, Patch
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