Version Differences for ALLPATHS-LG Data

(→100X)
(→S. pneumoniae)
Line 122:
  =S. pneumoniae=    =S. pneumoniae= 
  Streptococcus pneumoniae TIGR4. The S. pneumoniae TIGR4 consists of a circular chromosome of 2,160,842 bp in length.    Streptococcus pneumoniae TIGR4. The S. pneumoniae TIGR4 consists of a circular chromosome of 2,160,842 bp in length. 
       
    + ==Website data==  
    + The Illumina and pacbio data were downloaded from [ftp://ftp.broadinstitute.org/pub/papers/assembly/Ribeiro2012/data/rhody_data.tar.gz ALLPATHS-LG website] <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==  
    + 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