Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Kraken - why not working anymore SK-N-BE Bioinformatics 1 04-10-2018 11:06 PM
FASTQ read filtering/trimming/subsets ... a new approach kopardev Bioinformatics 3 01-17-2016 10:26 PM
filtering out human contaminants ruchi Metagenomics 3 03-01-2015 01:06 PM
Multiple read QC steps (trimming, filtering etc) in one go ... what's the best way? fahmida Bioinformatics 4 09-24-2014 03:27 PM
Read quality filtering for long, PE runs kmcarr Illumina/Solexa 0 07-21-2009 07:07 AM

Thread Tools
Old 02-04-2020, 05:56 AM   #1
Location: Hanover, Germany

Join Date: Sep 2018
Posts: 15
Lightbulb Human read filtering with Kraken 2

Hey everyone,

I was wondering something regarding the usage of Kraken 2 for read filtering.
I sequence/assemble viruses and inherited a pipeline in which human reads were removed by a simple Bowtie2 mapping to hg19.
While doing some metagenomic analysis of a sample with Kraken 2, I noticed how fast it was, so I build a Kraken database with just the human genome and tried filtering my reads with that. I tested it on a sample with around 2 million reads which we already assembled previously.

Filtering with Kraken was ~10x faster and both methods removed roughly half of the reads. Kraken, however, removed ~6k reads more, 2k of which seemed to be viral (985k of the remaining 1028k reads reads mapped to the assembled virus consensus, compared to 987k of the remaining 1034k reads with Bowtie).

I looked online but found noone who (mis)uses Kraken that way. The database is even smaller than the indexed hg19 for Bowtie. Am I missing something? At least, I feel a little bad for Kraken (if I'm allowed to anthropomorphise a bit) as it provides me with all this taxonomic data which I'm completely ignoring.

Last edited by JasperGeh; 02-04-2020 at 06:02 AM.
JasperGeh is offline   Reply With Quote
Old 02-04-2020, 06:00 AM   #2
Senior Member
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,101

Have you looked at this:
GenoMax is offline   Reply With Quote
Old 02-05-2020, 11:36 PM   #3
Location: Hanover, Germany

Join Date: Sep 2018
Posts: 15

Yes, I have stumbled upon that but haven't tried it yet. Is that the "gold standard" for human read removal, if there is something like that?
JasperGeh is offline   Reply With Quote

bowtie, filtering, kraken

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 11:30 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO