Issue interpreting plasmidSPAdes output
0
0
Entering edit mode
3.9 years ago
A_heath ▴ 160

Hi all,

I am using plasmidSPAdes for plasmid prediction on raw sequencing datas.

I ran the following command:

spades.py -o PlasmidSPades_results -1 R1_raw_reads.fastq -2 R2_raw_reads.fastq --plasmid

The program works fine but I'm having trouble interpreting the output files.

Indeed, on the file named contigs.fasta, I have several contigs with the id: component_X. Here is an example:

>NODE_1_length_43010_cov_119.234319_component_0
GCGCGTCGCCGAGCTTGTCGAGC ...
>NODE_20_length_950_cov_73.572738_component_1
TTGCTCAGCTTGTCGGTGGCTTGCCA ...
>NODE_5_length_11025_cov_340.981549_component_2
TATACGCAAATACGTATTTGCGTGATAC ...

I am assuming that because I have 3 different component IDs, my strain has 3 plasmids? Is that absolutely wrong?

If someone would help me interpreting plasmidSPAdes output, it would be very helpful!

Thank you in advance

Audrey

plasmidSPAdes • 1.1k views
ADD COMMENT
0
Entering edit mode

It's extremely rare to get "closed" or "complete" molecules with whatever assembler. Just three contigs would be an extremely low number for e.g. a bacterial genome assembly. I don't know what exactly plasmid spades does. However, just looking at the headers, the length of your second contig is only 950 nt. Can plasmids be that small?

ADD REPLY

Login before adding your answer.

Traffic: 1686 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6