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The Illumina sequencing data were available at [ftp://ftp.broadinstitute.org/pub/papers/assembly/Ribeiro2012/ ALLPATHS-LG website], Please refer to [http://www.ncbi.nlm.nih.gov/pubmed/22829535 ''Finished bacterial genomes from shotgun sequence data.'' Genome Research 2012] for detail.
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=E. coli=
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==Website data==
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The Illumina and pacbio data were downloaded from ALLPATHS-LG website : [ftp://ftp.broadinstitute.org/pub/papers/assembly/Ribeiro2012/data/ecoli_data_alt.tar.gz ecoli_data_alt.tar.gz] <br>
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===Fragment library===
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Reads length : 101bp <br>
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Reads amount : 1186190 X2 <br>
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Insert size : 180bp <br>
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Coverage : 46.02X
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===Jumping library 1===
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Reads length : 93bp <br>
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Reads amount : 1615702 X2 <br>
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Insert size : 3000bp <br>
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===Jumping library 2===
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Reads length : 93bp <br>
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Reads amount : 362199 X2 <br>
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Insert size : 3000bp <br>
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===PacBio reads===
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Reads average length : 1514.24bp <br>
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Reads amount : 409304 <br>
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Coverage : 133.58X <br>
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==Raw data==
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The raw data of website data from Sequence Read Archive (SRA)
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===Fragment library===
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Accession : [http://www.ncbi.nlm.nih.gov/sra/SRX131033 SRX131033] <br>
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Reads length : 101bp <br>
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Reads amount : 13457571 X2 <br>
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Insert size : 180bp <br>
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Coverage : 522.1X <br>
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===Jumping library 1===
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Accession : [http://www.ncbi.nlm.nih.gov/sra/SRX117481 SRX117481] <br>
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===Jumping library 2===
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Accession : [http://www.ncbi.nlm.nih.gov/sra/SRX145082 SRR492488] <br>
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===PacBio reads===
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Accession : [http://www.ncbi.nlm.nih.gov/sra/SRX109917 SRX109917], [http://www.ncbi.nlm.nih.gov/sra/SRX109901 SRX109901](SRR386913, SRR387092, SRR386907, SRR387035), [http://www.ncbi.nlm.nih.gov/sra/SRX109936 SRX109936]
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==Self-fraction data==
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We randomly selected the same fraction as website data from fragment library of raw data by prepare.sh.
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PrepareAllPathsInputs.pl\
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DATA_DIR=$PWD/test.genome/data\
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PLOIDY=1\
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FRAG_FRAC=0.088\
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IN_GROUPS_CSV=in_groups.csv\
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IN_LIBS_CSV=in_libs.csv\
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OVERWRITE=True\
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| tee prepare.out
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==100X fragment reads==
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We randomly selected 100X coverage data from fragment library of raw data by prepare.sh.
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Fraction = 100 / 522.1 = 0.192 <br>
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PrepareAllPathsInputs.pl\
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DATA_DIR=$PWD/test.genome/data\
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PLOIDY=1\
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FRAG_FRAC=0.192\
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IN_GROUPS_CSV=in_groups.csv\
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IN_LIBS_CSV=in_libs.csv\
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OVERWRITE=True\
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| tee prepare.out
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