Question: Metagenomics/De Novo Sequencing
1
gravatar for Mala
7.8 years ago by
Mala10
Mala10 wrote:

Hi,

I am new to NGS field and would appreciate help with a project. I receives fastq read file from a metagenome project(3 different species, virus) from Ion Torrent. What are the steps for proceeding with this data and which assembler gives best results when used for metagenomics.

My understanding is that the following are the 3 main steps to analyze this dataset

  1. Assembly
  2. BLAST the contigs
  3. Annotation and Functional analysis

Thanks Mala

ADD COMMENTlink modified 7.8 years ago by Obi Griffith18k • written 7.8 years ago by Mala10
1

Please describe your project a bit more. It is eather not a metagenome, or it contains more than 3 spicies. Also, viral metagenomics is quite different from bacterial, when it comes to taxonimic classification and community composition analysis.

ADD REPLYlink written 7.8 years ago by Michael Dondrup47k
1
gravatar for ALchEmiXt
7.8 years ago by
ALchEmiXt1.9k
The Netherlands
ALchEmiXt1.9k wrote:

Can't help you much whith this meta or Ion torrent specifically.

But I should definitely include a step zero:

Quality filtering of reads and sanitizing (discarding any non relevant reads known to be contaminants (like host derived sequences) by mapping using bowtie, bwa or....). This can significantly speed-up and improve the final quality of the assembly!

ADD COMMENTlink written 7.8 years ago by ALchEmiXt1.9k
0
gravatar for Obi Griffith
7.8 years ago by
Obi Griffith18k
Washington University, St Louis, USA
Obi Griffith18k wrote:

This question is maybe a little too big/broad. I recommend you start by reading the relevant literature. For example Wooley et al (2010) provide a very nice primer on metagenomics in PLoS Computational Biology and cover your three steps in detail with links/references to other relevant publications and tools. Once you get started, you might have more luck with posting more specific questions here.

ADD COMMENTlink written 7.8 years ago by Obi Griffith18k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1244 users visited in the last hour