Best Assembler for Metagenome Assembly

[chayan]

Hii All,

I have couple of questions regarding metagenomic assembly..

1. What is the best assembler (open source please!!) for a denovo or reference based assembly for iontorrent/proton reads?? i have tried MIRA4.0..any reference?

2. Is there a difference between reference based assembly and a mapping assembly?

3. As i am very new to this field and basically from a biology background so this question may sound silly, sorry for that... what is the easiest & quickest way to perform a binning for improving any meta-genomic assembly?? (well improving in terms of both long contigs as well as accuracy).. i have gone through several papers published in Science/PNAS/ISME..to be very honest, i am really confuse which one is the best and easy to tackle..any help??

Currently i am working with both iontorrent and ion-proton deep sequence reads..400bp chemistry for iontorrent (avg read length 195) and 200 bp chem for proton (176 avg read length)

4. What is the difference between binning and clustering (functional/taxonomic)??

5. Any tools or packages for functional binning?? or nucleotide based (as in k-mer frequency based)??

Thanks for any help in advance

Regards

Chayan

[TiborNagy]

I do not think there is any "best" assembler. For example Mira has a lots of parameters. I can create very bad assembly with Mira, if I use inproper input data or silly settings. Mira is a good tool, but it is not designed for metagenomics.

2. I think it has the same meaning.

3. Maybe RayMeta is a good tool, but I have not used it.

[krobison]

KHMER may be of interest to you as it is designed for filtering & binning large read sets such as would result from a metagenomic sample