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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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We 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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We have corrected the long read sequence data (200X) with illumina short reads (100X), with or without specifying genome size.
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We 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 miseq.100X.frg.bz2 |
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| depth: 199.81X||depth: 161.84X||depth: 40.14X |
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| depth: 199.81X||depth: 161.84X||depth: 40.14X |
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In addition to filter 25X PBcR for assembly, we used different Celera Assembler parameters as described in [http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=PacBioToCA ref].
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runCA -p asm -d asm -s asm.spec viaMiseq.frg
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runCA unitigger=bogart merSize=14 ovlMinLen=<ovl value> utgErrorRate=0.015 utgGraphErrorRate=0.015 utgGraphErrorLimit=0 utgMergeErrorRate=0.03 utgMergeErrorLimit=0 -p asm -d asm viaMiseq.frg
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