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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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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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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 -dumpfrg -longestlength 0 116250000 asm.gkpStore > 25X_Clr.frg
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=Dataset 5 (''E. coli'' K-12 MG1655, 17 SMRT cells)= |
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=Dataset 5 (''E. coli'' K-12 MG1655, 17 SMRT cells)= |
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We used all SMRT cells and randomly selected four, six and eight SMRT cells three times for each, and evaluated the assemblies by QUAST against the reference genome ([ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__MG1655_uid57779/ NC_000913]) and [[Media: Ec_gene_result.ncbi | Ec_gene_list]]. ([http://sb.nhri.org.tw/comps/quast/SCA/D5/report.html more detail]) |
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We used all SMRT cells and randomly selected four, six and eight SMRT cells three times for each, and evaluated the assemblies by QUAST against the reference genome ([ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__MG1655_uid57779/ NC_000913]) and [[Media: Ec_gene_result.ncbi | Ec_gene_list]]. ([http://sb.nhri.org.tw/comps/quast/SCA/D5/report.html more detail]) |
