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=S. pneumoniae=
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Streptococcus pneumoniae TIGR4. The S. pneumoniae TIGR4 consists of a circular chromosome of 2,160,842 bp in length.
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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/strep_data.tar.gz strep_data.tar.gz] <br>
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===Fragment library===
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Reads length : 101bp <br>
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Reads amount : 1067060 X2 <br>
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Insert size : 180bp <br>
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Coverage : 88.89X
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===Jumping library===
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Reads length : 93bp <br>
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Reads amount : 1161883 X2 <br>
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Insert size : 3000bp <br>
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===PacBio reads===
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Reads average length : 1159.12bp <br>
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Reads amount : 403745 <br>
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Coverage : 216.58X <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/SRX110128 SRX110128] <br>
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Reads length : 101bp <br>
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Reads amount : 5706200 X2 <br>
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Insert size : 180bp <br>
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Coverage : 475.33X <br>
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===Jumping library===
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Accession : [http://www.ncbi.nlm.nih.gov/sra/SRX105406 SRX105406] <br>
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===PacBio reads===
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Accession : [http://www.ncbi.nlm.nih.gov/sra/SRX109959 SRX109959],[http://www.ncbi.nlm.nih.gov/sra/SRX109958 SRX109958]
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==Self-fraction data==
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We randomly selected the same fraction as website data from fragment and jumping library of raw data by prepare.sh.
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PrepareAllPathsInputs.pl\
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DATA_DIR=$PWD/test.genome/data\
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PLOIDY=1\
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FRAG_FRAC=0.187\
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JUMP_FRAC=0.558\
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IN_GROUPS_CSV=in_groups.csv\
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IN_LIBS_CSV=in_libs.csv\
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OVERWRITE=True\
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| tee prepare.out
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==100X fragment reads==
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We randomly selected 100X coverage data from fragment library of raw data by prepare.sh.
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Fragment library fraction = 100/475.12 = 0.21 <br>
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PrepareAllPathsInputs.pl\
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DATA_DIR=$PWD/test.genome/data\
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PLOIDY=1\
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FRAG_FRAC=0.21\
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JUMP_FRAC=0.558\
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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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We also use another setting with all jumping library reads.
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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=0.21\
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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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