SPAdes - D1 and D5

We used Dataset 1, Escherichia coli K-12 MG1655 and with single SMRT cell long reads of Dataset 5 (m120208_071634)

spades.py --pe1-1 frag_1.fastq --pe1-2 frag_2.fastq --mp1-1 jump1_1.fastq --mp1-2 jump1_2.fastq --mp2-1 jump2_1.fastq --mp2-2 jump2_2.fastq --pacbio long.fasta -o output

spades.py --pe1-1 frag_1.fastq --pe1-2 frag_2.fastq --mp1-1 jump1_1.fastq --mp1-2 jump1_2.fastq --mp2-1 jump2_1.fastq --mp2-2 jump2_2.fastq -o output

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.