Version Differences for Dataset2
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(→Short reads)
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(→Data)
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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. | We combined MiSeq_Ecoli_MG1655_110721_PF_R1.fastq and MiSeq_Ecoli_MG1655_110721_PF_R2.fastq to MiSeq_PE.fastq. | ||
| - | The data in frg format were downloaded from [ftp://ftp.cbcb.umd.edu/pub/data/PBcR/closure_paper/K12/miseq.100X.frg.bz2 Miseq100X] | + | java convertFastqToFastaAndQual MiSeq_PE.fastq MiSeq_PE.fna MiSeq_PE.qual |
| - | == 118X (HQ) == | + | convert-fasta-to-v2.pl -mean 297 -stddev 35 -m Mate_info -l Illumia_Ecoli -s MiSeq_PE.fna -q MiSeq_PE.qual > MiSeq_PE.frg |
| + | The data in frg format were downloaded from [ftp://ftp.cbcb.umd.edu/pub/data/PBcR/closure_paper/K12/miseq.100X.frg.bz2 Miseq100X.frg] | ||
| We have trimmed the sequence reads to be of error probability less than 0.05. The paired-end reads were discarded if one read is shorter than 150bp. | We have trimmed the sequence reads to be of error probability less than 0.05. The paired-end reads were discarded if one read is shorter than 150bp. | ||
| - | We therefore obtained 1,839,935 paired-end reads (~118X) with high quality for further analysis. | + | We therefore obtained 1,839,935 paired-end reads (~118X, tMiSeq_PE) with high quality for further analysis. |
| - | java convertFastqToFastaAndQual MiSeq_PE.fastq MiSeq_PE.fna MiSeq_PE.qual | ||
| - | 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 | ||
| == Long reads == | == Long reads == | ||
| 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]. | 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]. | ||