Just to add my two pennies worth - pipelines for analysis of viromes:

VIROME: classification of predicted open-reading frames (ORFs) from viral metagenomes

METAVIR/METAVIR 2: tools for viral metagenome comparison and assembled virome analysis

Take a look at VMGAP and ProViDE as well.

May I add a plug for http://www.ebi.ac.uk/metagenomics? We have developed a pipeline for taxonomic and functional analysis of metagenomic samples and we also archive your raw sequence data in the SRA on your behalf. We're always looking for suggestions of how to improve our service, so please contact us with feedback. We will be launching new features on our website later next month and hope to publish the resource in NAR database issue this year.

Other (new) tools for metagenomic analysis:

• AmphoraNet: metagenomic analysis webserver
• AmphoraVizu: Chart visualization webserver for metagenomics analysis tools AMPHORA2 and AmphoraNet
• FANTOM: functional and taxonomic analysis of metagenomes
• MetaPhlAn: metagenomic phylogenetic analysis

MetAMOS

http://genomebiology.com/2013/14/1/R2

https://github.com/marbl/metAMOS

http://metamos.readthedocs.org/en/latest/

SURPI: Pipeline for pathogen identification from complex metagenomic NGS data.

http://chiulab.ucsf.edu/surpi/

http://genome.cshlp.org/content/early/2014/05/16/gr.171934.113.full.pdf+html

Cool new profiler tool for metagenomic data, ShortBRED.

ShortBRED is a pipeline to take a set of protein sequences, group them into families, extract a set of distinctive strings ("markers"), and then search for these markers in metagenomic data and determine the presence and abundance of the protein families of interest.

16S Metagenomics:

Mothur: https://www.mothur.org/wiki/Category:Commands

Usearch: http://www.drive5.com/usearch/manual/

Qiime: http://qiime.org/scripts/

Hi,

I recently find these two software pretty useful :

Gene Calling:

prodigal: http://prodigal.ornl.gov/server.html

pathway and function prediction:

picrust: http://picrust.github.io/picrust/

In the category "Microbial Diversity Analysis":

A very nice and frequently updated program in order to pick OTU from 16S rRNA gene amplicons sequencing: USEARCH (http://www.drive5.com/usearch/).

It is not user-friendly (command line), but the documentation is nice and the tools well adapter and flexible.

Recent input

ViraPipe: Scalable Parallel Pipeline for Viral Metagenome Analysis from Next Generation Sequencing Reads

ViraPipe in github

Check this out: https://omictools.com/metagenomics-category

They manage a curated list of bioinformatics tools.

From their site: "OMICtools strives to accelerate research in bioinformatics, making tools accessible to everyone and offering a stimulating work environment to assist life scientists extracting new findings from the omics data."

Have a look on Mash Screen, I found it usefull and easy to use!

You can try gaia.sequentiabiotech.com for free

16S Metagenomics:

in R

• DADA2 to Filter, quality analysis, trimming, Merge Runs, Remove Chimeras, Assign Taxonomy Phyloseq to
• Phyloseq to a deeper analysis of metagenomic data.

Gaia for analyzing both amplicon and shotgun metagenomics (including metatranscriptomics). Everything's done online.

I really liked using Centrifuge for WGS taxonomic profiling.

It is resource efficient (has a 6GB index for all bacteria, compared to Kraken's over 100GB) and produces an abundance table when it's finished.

16S rRNA metagenomics:

I tried DocMind Analyst on the AWS cloud and found it very convenient and easy to use. It works with a graphical user interface and uses mothur and RDP for read processing and classification. Their tutorials are also very good for beginners.

For virome assembly, the best results are obtained with s-aligner. It gets at least 64% larger NG50 than the second best.

Source: "s-aligner: a greedy algorithm for non-greedy denovo genome assembly"