Metagenomics/De Novo Sequencing

Question

[Mala]

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

[Michael]

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.

Answer 1

[ALchEmiXt]

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!

Answer 2

[Obi Griffith]

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.