I got sequences by metagenomics method for analysis, I am going by NCBI, BLAST analysis. Any best alternative rapid and good software available to analisis of this sequences.
list of tools and links to a few of them , that can be used for primary and secondary analysis of metagenomic sequence data.
Sequence similiarity based binning
MEGAN http://ab.inf.uni-tuebingen.de/software/megan/
CARMA http://www.cebitec.uni-bielefeld.de/brf/carma/carma.html
Phymm http://www.cbcb.umd.edu/software/phymm/
Biomedical : Online Software for Sequence Analysis
http://www.science.co.il/Biomedical/Sequence-Tools.asp
A goood tool in this case is Metawatt binner (The binning of metagenomics contigs for microbial physiology of mixed culture. Strous et al., 2012, Frontiers in Microbiol.)
if you have no computational power, just go for MG-RAST and work your assembly and pre-assembly work on Galaxy.
I agree with X. Bailly, one of the best tools you can use is Mothur. And now, there is an 'interface' version (in java) that avoids the need for command line. Moreover, it presents several implemented pipelines that you can use for whatever you need: 16S 454, 16S Illumina, proteins...
You can also use QIIME, another tool that gather some other software scripts, ready to use by command line.
If you are used to R you can also use the Bioconductor package, that allows you to do almost everything you need and is in continous growth, as it is an open source package.
Finally, you can install a LINUX OS with preinstalled bioinformatic tools called 'BioLinux'. When you get used to it, it is as easy as Windows.
Regards
I would say Qiime is the best available and free software now. I understand that if you not familiar with Command line or Linux it might seem difficult but I think it worth the try
If you need any help with qiime and how to get started or even how to analyze you data let me know
Good luck
Ahmed
I would suggest Gaia, which is an end to end, automated online software for amplicon-sequencing metagenomics (16S/18S/ITS), Whole Genome Sequencing (WGS) metagenomics and metatranscriptomics. It's commercial, but there is 2GB available for free (~40 amplicon-sequencing samples, ~2-4 WGS samples).
It is available in https://metagenomics.sequentiabiotech.com/.
Best,
Andreu
1. The first step of metagenomic data analysis requires the execution of certain pre-filtering steps, including the removal of redundant, low-quality sequences and sequences of probable eukaryotic origin.The methods available for the removal of contaminating eukaryotic genomic DNA sequences include Eu-Detect and DeConseq.
2. Assembly :DNA sequence data from genomic and metagenomic projects are essentially the same, but genomic sequence data offers higher coverage while metagenomic data is usually highly non-redundant.There are several assembly programs, most of which can use information from paired-end tags in order to improve the accuracy of assemblies. Some programs, such as Phrap or Celera Assembler, were designed to be used to assemble single genomes but nevertheless produce good results when assembling metagenomic data sets.
3. Gene prediction: The first approach is to identify genes based upon homology with genes that are already publicly available in sequence databases, usually by BLAST searches. This type of approach is implemented in the program MEGAN4.The second, ab initio, uses intrinsic features of the sequence to predict coding regions based upon gene training sets from related organisms. This is the approach taken by programs such as GeneMark and GLIMMER.
4. You can also study species diversity.
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