E. coli

Dataset 1, Escherichia coli K12 MG1655. This dataset includes three libraries: fragment, jump and long reads. The E. coli MG1655 consists of a circular chromosome of 4,639,675 bp in length. 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 : ecoli_data_alt.tar.gz

Fragment library
Reads length : 101bp
Reads amount : 1186191 X2
Insert size : 180bp
Coverage : 51.6X

Jumping library 1
Reads length : 93bp
Reads amount : 1615703 X2
Insert size : 3000bp

Jumping library 2
Reads length : 93bp
Reads amount : 362200 X2
Insert size : 3000bp

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

Raw data

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

Fragment library
Accession : SRR447685
Reads length : 101bp
Reads amount : 13457571 X2
Insert size : 180bp
Coverage : 585.9X
Jumping library 1
Accession : SRR401827

Jumping library 2
Accession : SRR492488

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 

library_name,  project_name,  organism_name,      type,  paired,  frag_size,  frag_stddev,  insert_size,  insert_stddev,  read_orientation,  genomic_start,  genomic_end
Solexa-36226,    hybrid_egg,            egg,  fragment,       1,        180,           15,             ,               ,            inward,              0,            0
Solexa-62929,    hybrid_egg,            egg,   jumping,       1,           ,             ,         3000,            600,          out ward,              0,            0
      pacbio,    hybrid_egg,            egg,      long,       0,           ,             ,             ,               ,                  ,              0,            0

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=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 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=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 v2.3)

Running QUAST requires Ec_gene_list and NC_000913.fna. There are 4497 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.