Question: Scaffolding for metagenomics
0
gravatar for David
3.1 years ago by
David150
David150 wrote:

Hi,

I have a quick question.

I have found a paper describing the different assembly tools http://www.ncbi.nlm.nih.gov/pubmed/24581555  "A comprehensive evaluation of assembly scaffolding tools"

It turns out that they have test abyss-map v1.3.6 which turns out to be a bit old now.

 

My question is if you recommend to use abyss for metagenomics scaffolding. Right now i´m using megahit and soapdenovo , soapdenovo is not maintained any more so i´m looking for other open source options.

Do you recommend abyss for metagenomics (human microbioe, soil, water...).

 

Thanks for sharing your experience

 

david

 

abyss assembly • 1.3k views
ADD COMMENTlink modified 3.0 years ago by Antonio R. Franco4.0k • written 3.1 years ago by David150
2

Hi David,

It is probably best to use an assembler/scaffolder that has been specifically designed and tested for metagenomic data.  (To the best of my knowledge, ABySS is not well tested for that application.)  I did a Google search for "metagenome assembler" and came across the following tools list from https://bioinformatictools.wordpress.com/tag/metagenomic-assembly/

* MetaVelvet

* MetAMOS

* IDBA-UD

* Meta-IDBA

* Ray Meta

* MAP

* Genovo

* Extended Genovo

* SmashCommmunity

* Bambus2

* MetaCAA

Maybe one of those tools will have a scaffolding module that you can use.

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by benv710
0
gravatar for Antonio R. Franco
3.0 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.0k wrote:

I would definitely recommend the using of a bunch of true mate paired sequences under these circumstances to do scaffolding. There are many reasons to rely in their use more than in pure assembly

ADD COMMENTlink written 3.0 years ago by Antonio R. Franco4.0k
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