SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics
Similar Threads
Thread Thread Starter Forum Replies Last Post
Custom trimming of "staggered" adapter sequences Bubblepig Bioinformatics 1 08-31-2015 05:09 AM
About adapter trimming starchildcn Illumina/Solexa 1 04-28-2015 07:28 AM
Adapter trimming and trimming by quality question alisrpp Bioinformatics 5 04-08-2013 04:55 PM
adapter trimming - help a_mt Bioinformatics 6 11-12-2012 07:36 PM
3' Adapter Trimming caddymob Bioinformatics 0 05-27-2009 12:53 PM

Reply
 
Thread Tools
Old 09-19-2016, 04:11 AM   #1
ecSeq Bioinformatics
Senior Member
 
Location: Leipzig, Germany

Join Date: May 2012
Posts: 305
Exclamation Trimming adapter sequences - is it really necessary?

Removal of adapter sequences in a process called read trimming, or clipping, is one of the first steps in analyzing NGS data. With more than 30 published adapter trimming tools there is a more than large choice for the appropriate tool. Yet, there is a debate whether this step really is as important as the number of tools suggests, or whether it is possible to skip this time-consuming step for many NGS applications. read more

Interesting discussion on biostars.org

__________________
ecSeq Bioinformatics is Europe’s leading provider of hands-on bioinformatics workshops and professional data analysis in the field of Next-Generation Sequencing (NGS).
ecSeq Bioinformatics is offline   Reply With Quote
Old 09-20-2016, 12:58 AM   #2
JulianTF
Junior Member
 
Location: Perth, Western Australia

Join Date: Apr 2013
Posts: 1
Default

Saving time by not pre-trimming before mapping / assembling, means time is going to be added back into the pipeline downstream. In the case of assembly, it will likely be added in with interest.

Not trimming before assembly means a graph-based assembler will face greater complexity, take longer to run and require more memory. When it finally prunes low traffic edges and dead-ends in the graph, then it's effectively trimming at that time which is a far more complicated way to get to the same point as a pre-trim -> assembly, so I doubt there's any time saving.

Given that an assembler and trimmer are both I/O bound when reading in data and that both are typically streaming input, then they can be piped. The worst bottleneck (disk I/O) can be reduced from R->W->R->W to just R->W. Because trimming is so computationally simple (we're not compute bound on trimming), then injecting a battle-tested pre-trim step between the disk and assembler input adds minimal time to the overall process.

Not trimming before mapping has some merit because a trailing adapter will rarely throw off the alignment and, post-alignment, it's even easier to confidently spot an adapter even if it has some miscalls in it. It does add complexity for PE mapping though, particularly if the reads cross over. An unsophisticated mapper will drop data because of this.

However, a trimming step is still going to have to be done after mapping instead of before, so where's the time saving? Taking the alignment into consideration during a post-trim is required (otherwise it's no different to a pre-trim). This means added memory and time unless the mapper has integrated trimming.

If depth is very high (eg, organelle sequencing), then one can always leave the adapters in, not bother post-trimming and set higher filters for variant calling. Once more, adding downstream complexity and noisy data that could have been avoided by a pre-trim.

Overall, I don't think the case against pre-trimming is particularly strong.

Last edited by JulianTF; 09-20-2016 at 01:02 AM.
JulianTF is offline   Reply With Quote
Old 09-20-2016, 01:39 AM   #3
Dornfield
Member
 
Location: Oxford

Join Date: Aug 2010
Posts: 11
Default Physical removal of adapter/ primer sequences

Slightly off topic, but definitely related, I've been doing a little hunting on the physical removal of the remnants of adapters or, more likely, the primer remnants of a library generated by targeted amplification. I'm only aware of the Thermo (Ion Torrent) AmpliSeq method of removing this remnant, with the (still mysterious?) FuPa reagent partially digesting the primer remnants away, such that when the A and P1 adapters are ligated, the known primer sequences are not interrogated. Are there other methods that achieve the same thing that I am unaware of? Searching variants of "primer remnant removal" brings back endless hits on how to do this in silico, but I am interested in other methods that achieve it in vitro.
Perhaps this is only an issue for Ion Torrent, due to the length of time required to flow individual dNTPs, and the fact that the highest quality sequence early in the run is otherwise sacrificed to the generation of sequences that are already known and are uninformative?
Dornfield is offline   Reply With Quote
Old 02-07-2017, 01:11 PM   #4
mlirski
Junior Member
 
Location: Warsaw, Poland

Join Date: Jun 2016
Posts: 4
Default

Just try some of the removal tools and see if teh adapter sequences are indeed there... I did it multiple times with reads from Proton and always found that there is not much to trim, likely just random occurences of sequences identical to part of the adapter. Such result was expected - the adapters are removed during basecalling. See: http://195.70.210.91/ion-docs/Techni...g_6455370.html
If the sequenced part of the adapter is shorter than 6 bp it will be ignored.
mlirski is offline   Reply With Quote
Reply

Tags
adapter trimming, ngs

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off



All times are GMT -8. The time now is 07:46 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO