Spades command for single cultivator

Question

[bioinfo223]

Hi, How to give spades command for multiple fastq files for a single cultivator.

spades.py -t 30 -1 ERR142_1.fastq -1 ERR143_1.fastq -2 ERR142_2.fastq -2 ERR143_2.fastq -o /SPADES_OUT/S_S002

Pl, let me know whether this command is right. I have one cultivator which has two fastq paired files, so I need a single assembly of this.

 spades.py -t 30 -1 ERR142_1.fastq, ERR143_1.fastq -2 ERR142_2.fastq, ERR143_2.fastq -o /SPADES_OUT/S_S002

If I am using this command it is giving me error.

Answer 1

[iraun]

According to Spades manual, under Specifying multiple libraries section, maybe something like this?

--pe1-1 ERR142_1.fastq --pe1-2 ERR143_1.fastq --pe2-1 ERR142_2.fastq --pe2-2 ERR143_2.fastq