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. 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 : rhody_data.tar.gz

Fragment library
Reads length : 101bp
Reads amount : 4354215 X2
Insert size : 180bp
Coverage : 170.16X
Jumping library
Reads length : 101bp
Reads amount : 1974031 X2
Insert size : 3000bp
PacBio reads
Reads average length : 1031.19bp
Reads amount : 1994107
Coverage : 446.44X

Raw data

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

Fragment library
Accession : SRX000946
Reads length : 101bp
Reads amount : 11339101 X2
Insert size : 180bp
Coverage : 433.12X
Jumping library
Accession : SRX111018
PacBio reads
Accession : SRX109847(SRR386702), SRX109812,SRX109830,SRX109818(SRR386746),SRX111329

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 fragment 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=4600000\
FRAG_COVERAGE=50\
JUMP_COVERAGE=50\
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 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 v2.2)

Running QUAST needs gene and sequence information. There are 4438 genes in total.

• Score with QUAST: With PacBio Long Reads more detail

• Score with QUAST: Without PacBio Long Reads more detail