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.

Contents [hide]

1 E. coli 1.1 Website data 1.1.1 Fragment library 1.1.2 Jumping library 1 1.1.3 Jumping library 2 1.1.4 PacBio reads 1.2 Raw data 1.2.1 Fragment library 1.2.2 Jumping library 1 1.2.3 Jumping library 2 1.2.4 PacBio reads 1.3 Self-fraction data 1.4 100X fragment reads 2 R. sphaeroides 2.1 Website data 2.1.1 Fragment library 2.1.2 Jumping library 2.1.3 PacBio reads 2.2 Raw data 2.2.1 Fragment library 2.2.2 Jumping library 2.2.3 PacBio reads 2.3 Self-fraction data 2.4 100X fragment reads 3 S. pneumoniae 3.1 Website data 3.1.1 Fragment library 3.1.2 Jumping library 3.1.3 PacBio reads 3.2 Raw data 3.2.1 Fragment library 3.2.2 Jumping library 3.2.3 PacBio reads 3.3 Self-fraction data 3.4 100X fragment reads

E. coli

Website data

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

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 1

Accession : SRX117481

Jumping library 2

Accession : SRR492488

PacBio reads

Accession : SRX109917, SRX109901(SRR386913, SRR387092, SRR386907, SRR387035), SRX109936

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 fragment reads

We randomly selected 100X coverage data from fragment library of raw data by prepare.sh.

Fraction = 100 / 522.1 = 0.192

PrepareAllPathsInputs.pl\
DATA_DIR=$PWD/test.genome/data\
PLOIDY=1\
FRAG_FRAC=0.192\
IN_GROUPS_CSV=in_groups.csv\
IN_LIBS_CSV=in_libs.csv\
OVERWRITE=True\
| tee prepare.out 

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.

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 : 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

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=0.384\
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 of raw data by prepare.sh.

Fraction = 100/443.12 = 0.226

PrepareAllPathsInputs.pl\
DATA_DIR=$PWD/test.genome/data\
PLOIDY=1\
FRAG_FRAC=0.226\
IN_GROUPS_CSV=in_groups.csv\
IN_LIBS_CSV=in_libs.csv\
OVERWRITE=True\
| tee prepare.out 

S. pneumoniae

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

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 : 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

Self-fraction 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 

100X fragment reads

We randomly selected 100X coverage data from fragment library of raw data by prepare.sh.

Fragment library fraction = 100/475.12 = 0.21

PrepareAllPathsInputs.pl\
DATA_DIR=$PWD/test.genome/data\
PLOIDY=1\
FRAG_FRAC=0.21\
JUMP_FRAC=0.558\
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\
FRAG_FRAC=0.21\
IN_GROUPS_CSV=in_groups.csv\
IN_LIBS_CSV=in_libs.csv\
OVERWRITE=True\
| tee prepare.out