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Short reads: 100X, long reads: 200X, w/wo genome size
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We have re-run correction and assembly with the data provided in [http://www.cbcb.umd.edu/software/PBcR/closure/ PBcR closure project].
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pacBioToCA -l viaMiseq -s pacbio.spec -t 10 -partitions 200 fastqFile=filtered_subreads.200X.fastq.bz2 miseq.100X.frg.bz2
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We have corrected the long read sequence data (200X) with illumina short reads (100X), with or without specifying genome size.
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pacBioToCA -l viaMiseq -s pacbio.spec -t 10 -partitions 200 fastqFile=filtered_subreads.200X.fastq.bz2 miseq.100X.frg.bz2
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pacBioToCA -l viaMiseq -s pacbio.spec -t 10 -partitions 200 fastqFile=filtered_subreads.200X.fastq.bz2 genomeSize=4650000 miseq.100X.frg.bz2 |
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pacBioToCA -l viaMiseq -s pacbio.spec -t 10 -partitions 200 fastqFile=filtered_subreads.200X.fastq.bz2 genomeSize=4650000 miseq.100X.frg.bz2 |
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| align="center" style="background:#f0f0f0;"|'''200X filtered long reads'''
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| align="center" style="background:#f0f0f0;"|'''Without genomeSize'''
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| align="center" style="background:#f0f0f0;"|'''genomeSize=4650000'''
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| seqs amount:383482||seqs amount:332880||seqs amount:37879
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| seq avg len:2422.877720||seq avg len:2260.68262||seq avg len:4927.683492
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| total:929.13 Mb||total:752.54 Mb||total:186.66 Mb
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| depth: 199.81X||depth: 161.84X||depth: 40.14X
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