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Self-correction approach (SCA) was proposed in the [http://www.ncbi.nlm.nih.gov/pubmed/24034426 ref] (''Reducing assembly complexity of microbial genomes with single-molecule sequencin'', Genome Biology 2013). |
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Self-correction approach (SCA) was proposed in the [http://www.ncbi.nlm.nih.gov/pubmed/24034426 ref] (''Reducing assembly complexity of microbial genomes with single-molecule sequencin'', Genome Biology 2013). |
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We Following we used ''E. coli'' as an example.
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Following we used ''E. coli'' as an example to show the steps
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1. Long reads self-correction
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pacBioToCA -length 500 -partitions 200 -l pacbio -t 6 -s ../pacbio.spec -fastq Filtered_four.fastq longReads=1 genomeSize=4650000 |
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pacBioToCA -length 500 -partitions 200 -l pacbio -t 6 -s ../pacbio.spec -fastq Filtered_four.fastq longReads=1 genomeSize=4650000 |
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python trimFastqByQVWindow.py --qvCut=54.5 --out=trimmed.pacbio.fastq ../pacbio.fastq
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2. Trimming corrected long reads
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python trimFastqByQVWindow.py --qvCut=54.5 --out=trimmed.pacbio.fastq pacbio.fastq
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java convertFastqToFastaAndQual ../trimmed.pacbio.fastq ../trimmed.pacbio.fasta ../trimmed.pacbio.qual
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3. Convert the data format from fastq to frg
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java convertFastqToFastaAndQual trimmed.pacbio.fastq trimmed.pacbio.fasta trimmed.pacbio.qual
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convert-fasta-to-v2.pl -l Pacbio -s trimmed.pacbio.fasta -q trimmed.pacbio.qual > trimmed.pacbio.frg |
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convert-fasta-to-v2.pl -l Pacbio -s trimmed.pacbio.fasta -q trimmed.pacbio.qual > trimmed.pacbio.frg |
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4. Select 25X longest corrected long reads
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gatekeeper -T -F -o asm.gkpStore trimmed.pacbio.frg |
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gatekeeper -T -F -o asm.gkpStore trimmed.pacbio.frg |
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gatekeeper -dumpfasta 25X_Clr -longestlength 0 116250000 asm.gkpStore |
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gatekeeper -dumpfasta 25X_Clr -longestlength 0 116250000 asm.gkpStore |
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runCA -p asm -d asm -s ../asm.spec 25X_Clr.frg |
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runCA -p asm -d asm -s ../asm.spec 25X_Clr.frg |
