1) The sequence data is in contigs form.
2) Please suggest windows based tools.
3) Important literature/source would also be appreciated.
Hi Ali, You may use the MG-RAST which is web-based tool or QIIME (not sure about the platform dependencies, runs on Linux though). If this is not useful you need to blast your contigs against 16s rRNA database like SILVA or Greengenes might be useful. Thanks!
Use PGAP: pan-genomes analysis pipeline. for a comprehensive analysis.
Linux based
For Eukaryotic genomes try CEGMA ( http://korflab.ucdavis.edu/datasets/cegma/ ). Unfortunately it is hard to install.
Cheers Chris
thanks to all for their contributions. However, I am looking for some windows based software, if someone can help me.
@ Dear Krzysztof stojecki, our laboratory has some bacterial genomes. Do you have any idea for this?
I think the easy to use is RAST ( http://www.nmpdr.org/FIG/wiki/view.cgi/FIG/RapidAnnotationServer ) and should work well with bacteria genomes. You can also try KAAS (http://www.genome.jp/tools/kaas/ ), but it's harder to refine informations from it.
After you have blasted your reads, you can use MEGAN.
try Gegeneees, its fairly easy to use... http://www.gegenees.org/download.html
EDGAR is great web-based software framework for such a case. Take a look on: http://www.ncbi.nlm.nih.gov/pubmed/19457249 and
http://www.ncbi.nlm.nih.gov/pubmed/22505676
PanOCT is worth a gander:
http://www.ncbi.nlm.nih.gov/pubmed/22904089
First of all, it would make me feel easier to provide a useful answer if you could specify what the purpose to use the pan-genome.
To the top of my head, most of the NGS tools for local usage are linux based. in that case u have to learn linux or go with the web-based tools. Agree with others, I will also suggest MG-RAST or GALAXY. And there is Java based tools are compatible with Windows platforms like MEGAN, Genenious, CLCbio Genomic Workbench (the latter two are commercial tools)
You may try with PANNOTATOR: an automated tool for annotation of pan-genomes
Hi,
I'm also would like to suggest the pannotator because there is an option to submit just one trustable genome as the source of annotation. For a while, please, use the below temporary site because the official website is under maintenance to substitute the old version for a new one. The current version supports a multlfasta file to be annotated, and each fasta will be separately annotated.'
BTW, in the below site just ignore the re-captcha resource.
Regards,
Anderson Santos
http://pannotator.facom.ufu.br
I agree with Anderson!
Our PANNOTATOR which is recently cited in NAR will be able to do the required analysis: Use this URL http://200.131.206.232/pannotator/index.html
If any one use this tool. Please cite as:
Santos AR, Barbosa E, Fiaux K, Zurita-Turk M, Chaitankar V, Kamapantula B, Abdelzaher A, Ghosh P, Tiwari S, Barve N, Jain N, Barh D, Silva A, Miyoshi A, Azevedo V. PANNOTATOR: an automated tool for annotation of pan-genomes. Genet Mol Res. 2013; 12(3):2982-9. [PubMed: 24065654]
PGAP or other pan genome analysis tool generated file can be used as the input files for Pangp.
Get homologues and Roary are two very good options. Use panGP for regression analysis.
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