Question: Query Regarding 454 paired end Metagenomic Data
0
gravatar for subodh
5.4 years ago by
subodh0
Bionivid Technology Pvt. Ltd, Bengaluru
subodh0 wrote:

Hello,

I have 454 paired end sequencing data for Metagenomics. The hyper variable (V4-V6) regions of the 16S rRNA genes was amplified from the total DNA extracted from  each  samples using bacterial primer pair 515F and 1061R.  

560bp (V4-V6) + an adapter + barcode sequence = ~598bp 

I have to do the Quality Control (QC) for the samples and also want to do downstream analysis. 

Can anyone suggest me any tool for doing QC as well as for downstream analysis for paired end metagenome 454 data ? 

Also if someone can provide me universal adapter sequence for 454, it will be helpful.

Thanks in advance.

454 sequencing • 1.5k views
ADD COMMENTlink modified 5.4 years ago by marina.v.yurieva520 • written 5.4 years ago by subodh0
0
gravatar for Sej Modha
5.4 years ago by
Sej Modha4.7k
Glasgow, UK
Sej Modha4.7k wrote:

Hi,

For QC you can use PRINSEQ.

For metagenomics analysis, you could try MetAMOS pipeline.

ADD COMMENTlink modified 12 months ago by RamRS30k • written 5.4 years ago by Sej Modha4.7k

Hello Sej,

Thank you so much for your reply.

ADD REPLYlink written 5.4 years ago by subodh0
0
gravatar for marina.v.yurieva
5.4 years ago by
Farmington, CT
marina.v.yurieva520 wrote:

For QC you can use fastqc

For 16S analysis you'll have to join the reads (can use flash) and then use pipeline from QIIME or mothur

ADD COMMENTlink modified 12 months ago by RamRS30k • written 5.4 years ago by marina.v.yurieva520
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