SPAdes usge commandline

Question

[Optimist]

Hey guys,

I'm using SPAdes (version 3.13) for assembling Ion torrent reads of Klebsiella pneumoniae.

FastQC Report:

Filename KP.fastq

File type Conventional base calls

Encoding Sanger / Illumina 1.9

Total Sequences: 1603362

Sequences flagged as poor quality : 0

Sequence length: 25-584

%GC : 54

Commandline used: ./spades.py --iontorrent -s 'KP.fastq' -o spades_output_kP

Kindly give your inputs about the commandline usage

Thanks & regards Optimist

[Bastien Hervé]

The question is : what do you want for your analysis ? If you think that you inputed all options you need, run the command line and see how it goes.

If you're not sure about an option, explain why you're not sure to use it and we could discuss that.

http://cab.spbu.ru/files/release3.12.0/manual.html#sec3.2