Dear all,
I am working on Hot spring metagenomics and we have Ion torrent data. The size of data: 214 Mbp. We want to upload assembled data for IMG/M ER. Now IMG accept only assembled data. Which assembler simply works on my data in window based PC?
Hi Amitsinh!
If you have the ionTorrent system in your lab then you already will be having a server based assembly/ manipulation suite that came along with the system. That said system uses MIRA assembler with an easy to use web based GUI...
If you do not have the said system in your lab and you do not wish to get into the powerful yet intimidating command based approach then you might have to shell out a lot of money to get a windows based easy to use assembler.
Windows based Assemblers:
CLC Genomics Workbench
DNAStar Lasergene Genomics Suit
Geneious Genomics Suit...
Let me suggest you one thing, why do not you use MG-RAST ?
It accepts raw data AFAIK.
Good luck....
Hi AmitSinh
As suggested by Aditya it would be better that you use the assembler that comes with Iontorrent. However, they have upgraded it to Spades Assembler instead of MIRA which is also very good. However, as your data is metagenomic data none of them would work. you will have to assemble with Meta-velvet or such tools.
Hello Amitsinh,
You can try PEAR and it also available in galaxy tool shed on Galaxy. Find it under NGS: QC and manipulation.
Good luck...
http://sco.h-its.org/exelixis/web/software/pear/
https://usegalaxy.org/
Hi Chintan
As far as my knowledge PEAR is just a paired end read merging tool and not a genome assembly tool.
I would also suggest you to go with Meta-velvet, as suggested by Ms. Garima and Dr. Umashankar.
Hi Amitsinh. I would echo the response from Aditya above. You will have access to Torrent Suite software that comes with you Ion Torrent. I dealt with this data a lot, including for meta genomics. I am also an advocate for CLC BIO Genomics Workbench. Problem is that you have to pay for that. With your meta genomics data after assembly I would recommend the Metagenomics suite on EBI. So easy to use and produces good results.
Hi,
It is better to use multiple tools at initial stage of analysis for any metagenomics data. We have to see whether our interested genes are accurately assembled or still any gaps are there. So, for that we need to perform multiple assemblies with various tools (stand alone: CLC, Newbler or command line tools: Velvet, Meta-velvet with varying k-mer sizes) and then perform annotation for all assemblies and check how much percent of annotation is there for particular assembly. We have to see whether there are more of unclassified contigs or annotated contigs cover only a portion of gene. Based on that we decide the potential of assemblers specifically for our data.
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