SEQanswers

Go Back   SEQanswers > Applications Forums > Metagenomics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Scaffolding and assembly quality evaluation/visualisation tools? MikhailFokin Bioinformatics 2 06-04-2015 06:57 AM
NGS data management tools and analysis tools [email protected] Bioinformatics 1 09-22-2014 01:50 AM
Metagenomics tools? lflc Bioinformatics 3 11-27-2012 12:37 AM
Is there any tools better than blast in metagenomics research? hellsingwyk Core Facilities 2 10-15-2012 09:11 AM

Reply
 
Thread Tools
Old 02-09-2016, 12:40 AM   #1
danova
Member
 
Location: France

Join Date: Sep 2010
Posts: 27
Default Scaffolding tools for metagenomics ???

Hello,
Im currently working on paired end data (2*150) to build a metagenomics assembly.

So far im using the combination of megahit to build contigs and soapdenovo for scaffolding. soapdenovo is not mainained anymore.

Does anybody worked with other scaffolding tools ??? SSpace seem to do the job but its not opensource.

thanks for sharing your experience.

david

Last edited by danova; 02-09-2016 at 04:00 AM.
danova is offline   Reply With Quote
Old 02-09-2016, 08:19 AM   #2
fibar
Member
 
Location: Argentina

Join Date: Feb 2013
Posts: 19
Default

Hi,
We've been using Velvet-MetaVelvet for a same type of data set, and we are pretty happy with it.
Check steps at http://metavelvet.dna.bio.keio.ac.jp/
Cheers!
fibar is offline   Reply With Quote
Old 03-21-2016, 03:45 AM   #3
Markiyan
Member
 
Location: Cambridge

Join Date: Sep 2010
Posts: 86
Lightbulb You can give Newbler a try, but proper matepair would be essential for good res...

Dear David,

Newbler assembler (v3 or v2.8) actually has quite good scaffolding module, provided you give it good and properly preprocessed (cleaned) data in the fastq format...

Also any tool is limited to the range of the input data (max. 1.2kb for illumina shotgun),
So a proper matepair (or 454 PE is a must, if yours repeats are longer than 900bp.

See bellow for more info:
http://seqanswers.com/forums/showthread.php?t=62617

Markiyan.

Quote:
Originally Posted by danova View Post
Hello,
Does anybody worked with other scaffolding tools ??? SSpace seem to do the job but its not opensource.

david
Markiyan is offline   Reply With Quote
Old 07-20-2016, 07:53 AM   #4
bastianwur
Member
 
Location: Germany/Netherlands

Join Date: Feb 2014
Posts: 98
Default

Opera also scaffolds.

It might be recommendable to first to binning on the contigs and afterwards the scaffolding, because it might lead to better results (due to less ambiguous mapping within the bins)
bastianwur is offline   Reply With Quote
Reply

Tags
metagenomics, scaffold, scaffolding

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 08:46 PM.


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