S. pneumoniae

Dataset 3, Streptococcus pneumoniae TIGR4. This dataset includes three libraries: fragment, jump and long reads. The S. pneumoniae TIGR4 consists of a circular chromosome of 2,160,842 bp in length. Please refer to Finished bacterial genomes from shotgun sequence data. Genome Research 2012 for detail.

Website 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 : 99.8X

Jumping library
Reads length : 93bp
Reads amount : 1161884 X2
Insert size : 3000bp
Coverage : 100.0X

PacBio reads
Reads average length : 1159.12bp
Reads amount : 403745
Coverage : 216.6X

Raw data

The raw Illumina data were obtained from Sequence Read Archive (SRA).

Fragment library
Accession : SRR387335
Reads length : 101bp
Reads amount : 5706200 X2
Insert size : 180bp
Coverage : 533.4X

Jumping library
Accession : SRR364158
Coverage : 179.2X

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 data

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 data

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 v2.3)

Running QUAST needs gene list and NC_003028.fna information. There are 2301 genes in total.

• Score with QUAST: With PacBio Long Reads more detail

Misassemblies for Adobe reader.

• Score with QUAST: Without PacBio Long Reads more detail

Misassemblies for Adobe reader.