metagenome analysis of redundant data

usegalaxy.org support
#1

Hi All!
I am new in using the Galaxy and also for the analysis. I have redundant (not only for the 16S) sequencing metagenome data. Now I can find the tutorials regarding the 16S rRNA analysis but not for the redundant ones. Can anyone help me for any helping material?
As I have paired end illumina based nova sequencing of 151 bp and one file (R1) size is 3GB.

#2

and also which database is suitable for the redundant data assembly? like for 16S we use silva.fasta reference database but what when we have Metagenomics using random shotgun sequencing of DNA what is the database we cab use in galaxy?

#3

I dont know if I can help in any way but can you explain what you mean with redundant data?

#4

Like I dont have only the 16S but it is the shotgun metagenome reads.

#5

random shotgun sequencing

#6

It all depends one what your end goal is. If you want to classify/identify the species in your sample you could start with a tool like MetaPhlAn (maybe also kraken2). If you want something else you could start with looking for assembly methods and binning. The tool metaSPAdes and MaxBin2 could be a start.

Here some pages that could be usefull:

Maybe someone else can give a better answer but the goal that you want to achieve need to be more clear I think.

#7

Thanks for sharing the links i will look into them for the help.
yes I want to identify the species into my samples.
I am trying with kraken but it is saying that no database is Aavilable.

#8

can u explain what is the contig file and Input type file selection?