SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Adaptor Removal with Trimmomatic hamcan Bioinformatics 3 11-25-2016 08:10 AM
Adaptor removal, trimming, vs masking ramirob Bioinformatics 3 03-27-2013 11:31 PM
Ancient DNA adaptor removal and read merging jimmybee Bioinformatics 8 05-24-2012 08:40 PM
P1 adaptor vs. Multiplex P1 adaptor hfaoro SOLiD 0 03-26-2012 06:54 AM
Casava 1.7 demultiplex.pl slowness FredG Bioinformatics 1 06-17-2011 08:28 AM

Reply
 
Thread Tools
Old 11-22-2017, 12:45 PM   #1
cement_head
Senior Member
 
Location: Oxford, Ohio

Join Date: Mar 2012
Posts: 188
Default Post-demultiplex adaptor removal?

If one has demultiplexed dual index reads on a MiSeq AND included "adaptor removal" as part of the demultiplexing (on instrument), should one also run the FASTQ files through an adaptor removal programme, or is this just overkill?
cement_head is offline   Reply With Quote
Old 11-22-2017, 02:00 PM   #2
Biocomputronics
Junior Member
 
Location: USA

Join Date: Sep 2017
Posts: 4
Default

I would suggest running FastQC on the data. It is a program that measures a wide variety of quality metrics. That way you can see with your own eyes the data quality measures, including adapter sequence contamination.

https://www.bioinformatics.babraham....ojects/fastqc/
Biocomputronics is offline   Reply With Quote
Old 11-24-2017, 06:01 AM   #3
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,574
Default

@cement_head: If there are no remaining adapters then all you lost is some time. For miseq datasets you would need less than 30 min to scan/trim data with bbduk.sh from BBMap. You can then be sure that there would be no extraneous sequences remaining in your data. Especially important if you were doing any de novo work.
GenoMax is offline   Reply With Quote
Old 12-01-2017, 11:37 PM   #4
[email protected]
Member
 
Location: Shenzhen, China

Join Date: Aug 2015
Posts: 15
Default

I suggest fastp to do automatic adapter trimming, read filtering and quality control. fastp is developed in C++ with multi-threading support, it's ultra-fast.

fastp has following features:
1, filter out bad reads (too low quality, too short, or too many N...)
2, cut low quality bases for per read in its 5' and 3' by evaluating the mean quality from a sliding window (like Trimmomatic but faster).
3, trim all reads in front and tail
4, cut adapters. Adapter sequences can be automatically detected,which means you don't have to input the adapter sequences to trim them.
5, correct mismatched base pairs in overlapped regions of paired end reads, if one base is with high quality while the other is with ultra low quality
6, preprocess unique molecular identifer (UMI) enabled data, shift UMI to sequence name.
7, report JSON format result for further interpreting.
8, visualize quality control and filtering results on a single HTML page (like FASTQC but faster and more informative).
9, split the output to multiple files (0001.R1.gz, 0002.R1.gz...) to support parallel processing. Two modes can be used, limiting the total split file number, or limitting the lines of each split file.
10, support long reads (data from PacBio / Nanopore devices).

fastp creates reports in both HTML and JSON format.

HTML report: http://opengene.org/fastp/fastp.html
JSON report: http://opengene.org/fastp/fastp.json

fastp is an open source project at github: https://github.com/OpenGene/fastp
__________________
OpenGene(Libraries and tools for NGS data analysis),AfterQC(Fastq Filtering and QC)
FusionDirect.jl( Detect gene fusion), SeqMaker.jl(Next Generation Sequencing simulation)
chen@haplox.com is offline   Reply With Quote
Reply

Tags
adaptor trimming, demultiplex, miseq, nextera

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 02:14 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO