E. coli

Escherichia coli K12 MG1655. The E. coli MG1655 consists of a circular chromosome of 4,639,675 bp in length. 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 : 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

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=0.088\
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 jumping library by prepare.sh.

PrepareAllPathsInputs.pl\
DATA_DIR=$PWD/test.genome/data\
PLOIDY=1\
GENOME_SIZE=4640000\
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 jumping library by prepare.sh.

PrepareAllPathsInputs.pl\
DATA_DIR=$PWD/test.genome/data\
PLOIDY=1\
GENOME_SIZE=4640000\
FRAG_COVERAGE=100\
JUMP_COVERAGE=100\
IN_GROUPS_CSV=in_groups.csv\
IN_LIBS_CSV=in_libs.csv\
OVERWRITE=True\
| tee prepare.out 

Evaluation

• Benchmark genome

E. coli MG1655

• Evaluated by QUAST

QUAST (QUAST v2.2)

Running QUAST needs gene and sequence information. There are 4497 genes in total.

• Score with QUAST: With PacBio Long Reads more detail

• Score with QUAST: Without PacBio Long Reads more detail