Version Differences for R. sphaeroides

Line 1:
    + =R. sphaeroides =  
       
    + Rhodobacter sphaeroides strain 2.4.1. The R. sphaeroides 2.4.1 consists of two circular chromosomes of 3,188,609 bp and 943,016 bp, and five plasmids of 114,045 bp, 114,178 bp, 105,284 bp, 100,828 bp and 37,100 bp in length, respectively.  
    + ==Website data==  
    + The Illumina and pacbio data were downloaded from ALLPATHS-LG website : [ftp://ftp.broadinstitute.org/pub/papers/assembly/Ribeiro2012/data/rhody_data.tar.gz rhody_data.tar.gz] <br>  
       
    + ===Fragment library===  
    + Reads length : 101bp <br>  
    + Reads amount : 4354215 X2 <br>  
    + Insert size : 180bp <br>  
    + Coverage : 170.16X  
    + ===Jumping library===  
    + Reads length : 101bp <br>  
    + Reads amount : 1974031 X2 <br>  
    + Insert size : 3000bp <br>  
    + ===PacBio reads===  
    + Reads average length : 1031.19bp <br>  
    + Reads amount : 1994107 <br>  
    + Coverage : 446.44X <br>  
    + ==Raw data==  
    + The raw data of website data from Sequence Read Archive (SRA)  
       
    + ===Fragment library===  
    + Accession : [http://www.ncbi.nlm.nih.gov/sra/SRX000946 SRX000946] <br>  
    + Reads length : 101bp <br>  
    + Reads amount : 11339101 X2 <br>  
    + Insert size : 180bp <br>  
    + Coverage : 433.12X <br>  
    + ===Jumping library===  
    + Accession : [http://www.ncbi.nlm.nih.gov/sra/SRX111018 SRX111018] <br>  
    + ===PacBio reads===  
    + Accession : [http://www.ncbi.nlm.nih.gov/sra/SRX109847 SRX109847](SRR386702), [http://www.ncbi.nlm.nih.gov/sra/SRX109812 SRX109812],[http://www.ncbi.nlm.nih.gov/sra/SRX109830 SRX109830],[http://www.ncbi.nlm.nih.gov/sra/SRX109818 SRX109818](SRR386746),[http://www.ncbi.nlm.nih.gov/sra/SRX111329 SRX111329]  
    + ==Self-fraction data==  
    + We randomly selected the same fraction as website data from fragment library of raw data by prepare.sh.  
       
    + PrepareAllPathsInputs.pl\  
    + DATA_DIR=$PWD/test.genome/data\  
    + PLOIDY=1\  
    + FRAG_FRAC=0.384\  
    + IN_GROUPS_CSV=in_groups.csv\  
    + IN_LIBS_CSV=in_libs.csv\  
    + OVERWRITE=True\  
    + | tee prepare.out  
    + ==100X fragment reads==  
    + We randomly selected 100X coverage data from fragment library of raw data by prepare.sh.  
       
    + Fraction = 100/443.12 = 0.226 <br>  
       
    + PrepareAllPathsInputs.pl\  
    + DATA_DIR=$PWD/test.genome/data\  
    + PLOIDY=1\  
    + FRAG_FRAC=0.226\  
    + IN_GROUPS_CSV=in_groups.csv\  
    + IN_LIBS_CSV=in_libs.csv\  
    + OVERWRITE=True\  
    + | tee prepare.out