Query Regarding 454 paired end Metagenomic Data

Question

[subodh]

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

Answer 1

[Sej Modha]

Hi,

For QC you can use PRINSEQ.

For metagenomics analysis, you could try MetAMOS pipeline.

[subodh]

Hello Sej,

Thank you so much for your reply.

Answer 2

[marina.v.yurieva]

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