Entering edit mode
4.6 years ago
DanielC
▴
170
Dear Friends,
I have a FASTq file with reads from multiple phages. Could you please let me know how to extract and perform genome assembly of every phage in this fastq file? I have the experience of performing genome assembly on one phage in one FASTQ file but not for multiple phages in a fastq file. Thanks !
Do you know which phages are supposed to be present? If so you could split/bin your fastq data using something lime bbsplit.sh from BBMap suite. Then follow that up with individual assemblies.
If these are related phages then you are going to have some problem. It would be difficult to uniquely assign reads to individual bins in that case.
thanks for the response!
No, the phages are isolated from water taken from different locations. I dont know if it possible to detect the phage type from merely this information.
Since, we dont know what phage it could belong to, what would you suggest would be an efficient strategy to perform genome assembly of each phage in that fastq file? Thanks!
In light of that information best you could try to do is meta aseembly. Take a look at this paper for some insights.
If you don't have to assemble the genomes you could take a selection of phage genomes and try to identify reads that align to get an idea of which phages may be present.