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.

E. coli

Website data

The Illumina and pacbio data were downloaded from ALLPATHS-LG website

Fragment library

Reads length : 101bp
Reads amount : 1186190 X2
Insert size : 180bp
Coverage : 46.02X

Jumping library 1

Reads length : 93bp
Reads amount : 1615702 X2
Insert size : 3000bp

Jumping library 2

Reads length : 93bp
Reads amount : 362199 X2
Insert size : 3000bp

PacBio reads

Reads average length : 1514.24bp
Reads amount : 409304
Coverage : 133.58X

Raw data

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

Fragment library

Accession : SRX131033
Reads length : 101bp
Reads amount : 13457571 X2
Insert size : 180bp
Coverage : 522.1X

Jumping library one

Accession : SRX117481

Jumping library two

Accession : SRR492488

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=0.088\
IN_GROUPS_CSV=in_groups.csv\
IN_LIBS_CSV=in_libs.csv\
OVERWRITE=True\
| tee prepare.out 

100X

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.

S. pneumoniae

Streptococcus pneumoniae TIGR4. The S. pneumoniae TIGR4 consists of a circular chromosome of 2,160,842 bp in length.