98    ◾    Bioinformatics

After decompression, the program files will be in “SPAdes-3.15.4-Linux/bin” ­directory.

You will need to add the program path to “.bashrc” file to be able to use the SPAdes ­program

files from any directory.

export PATH=”/home/your_path/SPAdes-3.15.4-Linux/bin:$PATH”

Replace “your_path” with the correct path to the directory on your computer. After adding

the line, restart the terminal or use “source ~/.bashrc” for the change to take effect. You can

test the installation by running the following command on the Linux terminal command

line:

spades.py --test

The above command will assemble toy read data that comes with the program. The output

will be saved in “spades_test”, which are the typical SPAdes output files.

Remember that we have downloaded two FASTQ files for E. coli and we used them with

ABySS above. The two files were saved in “denovo/fastq”; run the following command on

the Linux command line while you are in the working directory “denovo”:

python spades.py \

--pe1-1 fastq/ERR1007381_1.fastq.gz \

--pe1-2 fastq/ERR1007381_2.fastq.gz \

--isolate \

-o spades_ecoli_ass

The above code assembles contigs and scaffolds from the paired-end reads in the input

FASTQ files and saves the output files in a new directory “spades_ecoli_ass”. The output

files include intermediate file used for the construction of contigs and scaffolds, log files,

contigs’ file, and scaffolds’ file in FASTA format. The latter represents the assembly.

SPAdes can perform hybrid de novo assembly using any of PacBio continuous long reads

(CLR) or Oxford Nanopore reads as input with Illumina or Ion Torrent reads. You will

need to use “--pacbio” option for the PacBio FASTQ file and “--nanopore” option for the

Oxford Nanopore FASTQ file. In the following example, first, we download four PacBio

SMRT FASTQ files “SRR801646”, “SRR801649”, “SRR801652”, and “SRR801638” for E. coli

K12. Second, we will use these four PacBio files with the Illumina short read files to assem-

ble E. coli genome with SPAdes program.

python spades.py \

--pe1-1 fastq/ERR1007381_1.fastq.gz \

--pe1-2 fastq/ERR1007381_2.fastq.gz \

--pacbio pacbio/SRR801646.fastq.gz \

--pacbio pacbio/SRR801649.fastq.gz \

--pacbio pacbio/SRR801652.fastq.gz \

--pacbio pacbio/SRR801638.fastq.gz \