S. pneumoniae

Streptococcus pneumoniae TIGR4. The S. pneumoniae TIGR4 consists of a circular chromosome of 2,160,842 bp in length. The Illumina sequencing data were available at ALLPATHS-LG website, Please refer to Finished bacterial genomes from shotgun sequence data. Genome Research 2012 for detail.

Published data

The Illumina and pacbio data were downloaded from ALLPATHS-LG website : strep_data.tar.gz

Fragment library
Reads length : 101bp
Reads amount : 1067060 X2
Insert size : 180bp
Coverage : 88.89X
Jumping library
Reads length : 93bp
Reads amount : 1161883 X2
Insert size : 3000bp
PacBio reads
Reads average length : 1159.12bp
Reads amount : 403745
Coverage : 216.58X

Raw data

The raw data of website data from Sequence Read Archive (SRA)

Fragment library
Accession : SRX110128
Reads length : 101bp
Reads amount : 5706200 X2
Insert size : 180bp
Coverage : 475.33X
Jumping library
Accession : SRX105406
PacBio reads
Accession : SRX109959,SRX109958

Fractional data

We randomly selected the same fraction as website data from fragment and jumping library of raw data by prepare.sh.

PrepareAllPathsInputs.pl\
DATA_DIR=$PWD/test.genome/data\
PLOIDY=1\
FRAG_FRAC=0.187\
JUMP_FRAC=0.558\
IN_GROUPS_CSV=in_groups.csv\
IN_LIBS_CSV=in_libs.csv\
OVERWRITE=True\
| tee prepare.out 

50X coverage reads

We randomly selected 50X coverage data from fragment library and 50X coverage data from jumping library by prepare.sh.

PrepareAllPathsInputs.pl\
DATA_DIR=$PWD/test.genome/data\
PLOIDY=1\
GENOME_SIZE=2165000\
FRAG_COVERAGE=50\
JUMP_COVERAGE=50\
IN_GROUPS_CSV=in_groups.csv\
IN_LIBS_CSV=in_libs.csv\
OVERWRITE=True\
| tee prepare.out 

We also use another setting with all jumping library reads.

PrepareAllPathsInputs.pl\
DATA_DIR=$PWD/test.genome/data\
PLOIDY=1\
JUMP_FRAC=1\
GENOME_SIZE=2165000\
FRAG_COVERAGE=50\
IN_GROUPS_CSV=in_groups.csv\
IN_LIBS_CSV=in_libs.csv\
OVERWRITE=True\
| tee prepare.out 

100X coverage reads

We randomly selected 100X coverage data from fragment library and 100X coverage data from jumping library by prepare.sh.

PrepareAllPathsInputs.pl\
DATA_DIR=$PWD/test.genome/data\
PLOIDY=1\
GENOME_SIZE=2165000\
FRAG_COVERAGE=100\
JUMP_COVERAGE=100\
IN_GROUPS_CSV=in_groups.csv\
IN_LIBS_CSV=in_libs.csv\
OVERWRITE=True\
| tee prepare.out 

We also use another setting with all jumping library reads.

PrepareAllPathsInputs.pl\
DATA_DIR=$PWD/test.genome/data\
PLOIDY=1\
IN_GROUPS_CSV=in_groups.csv\
GENOME_SIZE=2165000\
FRAG_COVERAGE=100\
IN_LIBS_CSV=in_libs.csv\
OVERWRITE=True\
| tee prepare.out 

Evaluation

• Benchmark genome

S. pneumoniae TIGR4

• Evaluated by QUAST

QUAST (QUAST v2.2)

Running QUAST needs gene and sequence information. There are 2301 genes in total.

• Score with QUAST: With PacBio Long Reads more detail

• Score with QUAST: Without PacBio Long Reads more detail