Question: QC prior to bacterial genome assembly
1
gravatar for Seraph
6 weeks ago by
Seraph0
Seraph0 wrote:

Hi all,

I am analyzing raw data of Illumina reads for bacterial (Wole Genome Sequencing) using tools on the galaxy website. I used trimmomatic, and trim-Galore to remove adapters and low-quality readers.

Fastqc analysis of trimmed reads gave me this report!

Summary

Basic statistics

Per base sequence quality

Per base sequence content

Sequence Length Distribution

Sequence Duplication Levels

Previously, I faced a problem with Nexttera Transposase sequences, but it was solved by using Trim-Galore as recommended,

1- So, Please give me your evaluation! Is it ok to use this reads for assembly!, or I should improve the quality!!, and how can I improve it!

2- Also, is it enough to assemble the paired reads, or I should also process unpaired ones as well!

Thank you for your time

sequencing next-gen genome • 166 views
ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by Seraph0
1

The link you posted is broken. I edited your title, please use short, meaningful titles in the future.

2- Also, is it enough to assemble the paired reads, or I should also process unpaired ones as well!

Depends on how much coverage you have, but generally, using just the paired ends is enough.

ADD REPLYlink written 6 weeks ago by h.mon30k

thanks, h.mon, I modified the post...

ADD REPLYlink written 6 weeks ago by Seraph0
1

The images still appear to be broken. Please post correct links.

ADD REPLYlink written 6 weeks ago by genomax87k

I re-uploaded the photos

ADD REPLYlink written 6 weeks ago by Seraph0
1

Don't set an auto-delete time, if you were doing that.

BTW: Data looks reasonable. If the adapters are gone then you can try doing the assembly.

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by genomax87k

I Modified it again, thanks

ADD REPLYlink written 6 weeks ago by Seraph0
1

1- So, how can I improve these results using galaxy tools, in which I can move to the assembly step

I don't know if you can provide custom sequences to trimmomatic via galaxy interface. But that would be the way to go to tackle.

Nextra Transposase sequences

I suggest that you use How to add images to a Biostars post to post images from FastQC report.

FastQC authors have some blog posts that are a good read to understand some of the observations you have noted.

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by genomax87k

thank you genomax for the link, it is very useful

ADD REPLYlink written 6 weeks ago by Seraph0
1

Nextra Transposase sequences are still there

If you are using galaxy you could try trimgalore. This tool already has a parameter specifically for Nextra Transposase

ADD REPLYlink written 6 weeks ago by gb1.9k

Thank you gb, I used trim-galore and it successfully removed these adapters

ADD REPLYlink written 6 weeks ago by Seraph0
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