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Old 10-01-2014, 01:23 AM   #1
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Location: Bantry/Dusseldorf

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Default Where do I start?! Bacterial rRNA sequencing

Good morning!!!

I am fairly new to the world of sequencing and bioinformatics! But as part of my PhD I am sequencing 16S rRNA to identify what bacterial consortia are present in some microalgal cultures I have!

The idea is to do Ion Torrent type sequencing of the V6 region to start identifying the bacterial consortia present.

From what I understand, we will then receive the raw data as FASTQ ( millions of reads (??)) which we then need to sort through using software such as TopHat then use rRNA databases such as SILVA to place the bacteria in a phylogenetic tree.

Do any of you have any advice of what software to use and what databases? What parameters must be set for ambiguity so my results are of a publishable quality (cross fingers)?

Any help to try and understand the bioinformatics side of things will be greatly appreciated!!

Have a lovely day all!!
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Old 10-01-2014, 04:18 AM   #2
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You would not be using TopHat for the analysis you describe since it is meant for analysis of expression data.

You are interested in microbial communities, so Qiime and Mothur will likely be what you will end up using. There are tutorials availalable for Qiime ( and Mothur (
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Old 10-01-2014, 07:07 AM   #3
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Thank you so much for pointing me in the right direction, GenoMax!

Have a lovely day!
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