Tool:Annocript: completely automated transcriptome annotation pipeline which can also identify putative lncRNAs

Question

[francescomusacchia]

Hi all!

Annocript is finally published! http://www.ncbi.nlm.nih.gov/pubmed/?term=annocript

It is a free tool that permits the annotation of transcriptomes with BLAST against UniProt proteins, CDD domains and rFam. It is completely automated and only requires a fasta transcriptome in input. It returns a tabular output and an HTML web page with R plots (GO, Pathways, domains) and statistics. A plugin, already included in the package, permits to execute differential expression analyses and GO, pathways enrichments of the significantly DE transcripts.

Download it here: https://github.com/frankMusacchia/Annocript

A google group is already set up to solve any problem with it!

Francesco

[lakshmi.bioinformatics]

thank you sir

I am not able to get the full paper access for the tool

[francescomusacchia]

The access to the paper is only under subscription or payment. Anyway everything is well described in the user guide here: https://github.com/frankMusacchia/Annocript/blob/master/GUIDE/INTRO.md

Hope is helpful

cheers

[lakshmi.bioinformatics]

thank you

[Ashutosh Pandey]

Please use "comment" section for trivial communications.

[francescomusacchia]

ok! I'm sorry!

[lakshmi.bioinformatics]

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[francescomusacchia]

This should be spam IMHO....

Anyway, I add only people I personally knew in my network. Goodbye

[saj98]

Hello Francesco

Do you have a demo showing how to use Annocript.

Best

Shaiam

Answer 1

[francescomusacchia]

Currently we have a detailed user guide and an example of usage at https://github.com/frankMusacchia/Annocript/blob/master/GUIDE/TUTORIAL.md

We also set up a google group to answer questions coming from users https://groups.google.com/forum/#!forum/annocript

Hope this is useful

Cheers,

Francesco

[ranjeet_maurya]

Hello Francesco,

I am looking for annotation of my denovo assembled genomic data. I have good experience with Annocript for transcriptomic data annotation. Could we use the Annocript for genomic data annotation and point me toward a different tools like Annocript do, for whole genome annotation. That would be much appreciated.

[francescomusacchia]

Dear Ranjeet, please take a look at Augustus (http://bioinf.uni-greifswald.de/augustus/). Even if I never used it, I know from colleagues that it is a reliable tool.

Cheers, Francesco

[Puli Chandramouli Reddy]

Dear Ranjeet, Currently I am working on annotation part of de novo assembled genome. I am using MAKER pipeline. It provides multiple tools to generate complete annotation (almost) and output in different formats starting from GFF3 and also has many supporting scripts such as converting MAKER output to Jbrowse compatible tracks. Here is the link for MAKER tutorial "http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014"

Best Mouli

[ranjeet_maurya]

Thanks Puli, for your response and much appreciated for your valuable advice.

Answer 2

[francescomusacchia]

Dear Ranjeet, please take a look at Augustus (http://bioinf.uni-greifswald.de/augustus/). Even if I never used it, I know from colleagues that it is a reliable tool.

Cheers, Francesco

[ranjeet_maurya]

Thanks Francesco, i knew about Augustus but i am searching for the tool other than the Augustus for comparision of annotated data of genome dataset like Annocript do all (Gene, sequences, GO, functional anotation, KEGG pathways, graphs etc.). Is there any reliable tool you know.