R. sphaeroides

Dataset 2, Rhodobacter sphaeroides strain 2.4.1. This dataset includes three libraries: fragment, jump and long reads. 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. 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 : rhody_data.tar.gz

Fragment library
Reads length : 101bp
Reads amount : 4354215 X2
Insert size : 180bp
Coverage : 191.0X

Jumping library
Reads length : 101bp
Reads amount : 1974031 X2
Insert size : 3000bp

PacBio reads
Reads average length : 1031.19bp
Reads amount : 1994107
Coverage : 446.4X

Raw data

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

Fragment library
Accession : SRR125492
Reads length : 101bp
Reads amount : 11339101 X2
Insert size : 180bp
Coverage : 497.3X

Jumping library
Accession : SRR388672

Fractional 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 

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=4610000\
FRAG_COVERAGE=50\
JUMP_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=4600000\
FRAG_COVERAGE=100\
JUMP_COVETAGE=100\
IN_GROUPS_CSV=in_groups.csv\
IN_LIBS_CSV=in_libs.csv\
OVERWRITE=True\
| tee prepare.out 

Evaluation

• Benchmark genome

R. sphaeroides 2.4.1

• Evaluated by QUAST

QUAST (QUAST v2.3)

Running QUAST requires gene list and reference genome. There are 4388 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.