This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to set FASTQ trimming parameters before de novo assembly of the birch chloroplast genome?

How to set FASTQ trimming parameters before de novo assembly of the birch chloroplast genome? How much to cut and filter? On what facts to rely on? And is it obligatory to scaffold the resultant contigs and remove gaps before putting contig to the annotation engine?

plant assembly denovo trimming fastq
• 1,156 views • link
written by oxfordsoccer • oxfordsoccer

You should only remove sequence that is extraneous (e.g. adapters etc). No other manipulations should be necessary. If your data looks to have bad Q-scores then you could trim data at Q20 (or Q25, if you want to be strict) level.

Remember this. If parts of the genome have not been sequenced (and are not present in your data) then no matter what you do, you are not going to be able to generate a complete assembly. Making and sequencing another library would be the only alternative there.

• 0 views • link
written by GenoMax GenoMax

Hello oxfordsoccer!

We believe that this post does not fit the main topic of this site.

Sorry only humans are allowed to post here.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

• 0 views • link
written by Michael Dondrup Michael Dondrup

0 answers

No answers yet.

Log in to answer this question.

More posts like this