SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
HiSeq X different insert size? JBKri Illumina/Solexa 5 11-05-2016 06:42 AM
1000bp insert size with Illumina TruSeq DNA PCR-Free Library prep kit Lovro Sample Prep / Library Generation 13 10-03-2016 11:10 AM
HiSeq insert size njlodato Sample Prep / Library Generation 0 09-04-2015 10:03 AM
Maximum insert size with Hiseq 3000 upendra_35 Illumina/Solexa 6 07-23-2015 03:44 AM
150bp-1.3kb insert size PE on HiSeq jmugford Illumina/Solexa 5 04-19-2012 07:43 PM

Reply
 
Thread Tools
Old 03-08-2017, 07:49 AM   #21
fanli
Senior Member
 
Location: California

Join Date: Jul 2014
Posts: 198
Default

You might find this benchmark to be helpful:
http://www.nature.com/articles/srep19233

My understanding is that you are better off using newer k-mer based approaches as opposed to BLAST. I've had reasonable success with kraken, although the memory requirements are somewhat onerous. You also have to be extremely careful about removing contaminant (aka human) sequences as these tend to get misclassified.

Another option is kallisto (https://github.com/pachterlab/metakallisto) but I have yet to be able to even build a database due to memory constraints.
fanli is offline   Reply With Quote
Old 03-08-2017, 07:51 AM   #22
SDPA_Pet
Senior Member
 
Location: US

Join Date: Apr 2013
Posts: 222
Default

Quote:
Originally Posted by fanli View Post
You might find this benchmark to be helpful:
http://www.nature.com/articles/srep19233

My understanding is that you are better off using newer k-mer based approaches as opposed to BLAST. I've had reasonable success with kraken, although the memory requirements are somewhat onerous. You also have to be extremely careful about removing contaminant (aka human) sequences as these tend to get misclassified.

Another option is kallisto (https://github.com/pachterlab/metakallisto) but I have yet to be able to even build a database due to memory constraints.
I will try. Can you gimme the Kraken link? Thanks.
SDPA_Pet is offline   Reply With Quote
Reply

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 06:13 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO