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-   -   survery: what assembler, gene prediction and gene annotation softwares do you use? (http://seqanswers.com/forums/showthread.php?t=29490)

Gorbenzer 04-19-2013 01:57 AM

survery: what assembler, gene prediction and gene annotation softwares do you use?
 
Hi everyone,
i'm going to analize some Ion Torrent metagenomic data and have read a lot of posts about different softwares but i have very limited time and can't decide what one to try first.

Anyone tryed different softwares and can say what's the best one?

Please post the ones you use so i can give them a try :)

I usually run assembly with MIRA and it's working excellently, expecially the last developmental version 3.9.x, so i was tinking to stick with this one for the assembly.

Any suggestion for gene prediction and gene composition analysis tools?

Thanks for the help!

rhinoceros 04-19-2013 03:23 AM

We've had good results with MetaIDBA. I'm burning to try metAMOS with SOAPdenovo. Also, have a look here.

Gorbenzer 04-19-2013 04:47 AM

Thanks for the reply, metAMOS pipeline i think it's worth a try, any other suite/pipeline or tools for analyze gene composition??

rhinoceros 04-19-2013 05:27 AM

Quote:

Originally Posted by Gorbenzer (Post 102360)
Thanks for the reply, metAMOS pipeline i think it's worth a try, any other suite/pipeline or tools for analyze gene composition??

Something like MG-RAST? Or more like local stuff? tRNAscan, FragGeneScan, standalone blast, blat, MEGAN, mothur, etc.. it really depends on what you plan to study..

Gorbenzer 04-19-2013 06:03 AM

Quote:

Originally Posted by rhinoceros (Post 102365)
Something like MG-RAST? Or more like local stuff? tRNAscan, FragGeneScan, standalone blast, blat, MEGAN, mothur, etc.. it really depends on what you plan to study..

Local would be great, we have two servers for our analysis.

I'd like to try all the different approaces:
- Try to assembly all the data to see if i can get draft genomes of a few highly present species;
- Try to assembly all the data, predict ORFs and annotate them to obtain the gene pool of the sample;
- Try to "annotate" all the single reads to find out what genes are higly represented in the sample.

I would love to try gene prediction and annotation (including GO, EC and pathway prediction if possible) softwares specific for metagenomic analysis.

Thx for the help!

rhinoceros 04-19-2013 08:28 AM

Quote:

Originally Posted by Gorbenzer (Post 102369)
Local would be great, we have two servers for our analysis.

I'd like to try all the different approaces:
- Try to assembly all the data to see if i can get draft genomes of a few highly present species;
- Try to assembly all the data, predict ORFs and annotate them to obtain the gene pool of the sample;
- Try to "annotate" all the single reads to find out what genes are higly represented in the sample.

I would love to try gene prediction and annotation (including GO, EC and pathway prediction if possible) softwares specific for metagenomic analysis.

Thx for the help!

Well in this case, you're pretty much doing what I'm doing then. I use FragGeneScan for predicting protein-coding genes from contigs. These I've blasted against ncbi's nr database. For tRNA prediction I used tRNAscan-SE (3 runs each optimized for one domain). rRNAs by blastn megablast against Silva's SSU and LSURef databases. The M5nr database will be updated quite soon. If you want to get GOs, KEGGs and such with just one search, I recommend you find out more about it. If you do your blasts with -outfmt 5 or 6 (recommended) flags, you can import your data into MEGAN for neat analyses and visualizations. For other ideas, perhaps look into what e.g. IMG/M and MG-RAST do in their pipelines.. don't forget to screen for human contamination..

Gorbenzer 04-22-2013 01:25 AM

thx so much! i'll try to get started with this software :)


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