bacteriophage genome assembly

Question

[najibveto]

hello i am working on new bacteriophage i isolated from a bacteria. so i extracted the DNA from bacteriophage after isolation of the later using cesium gradient. i checked the DNA on electrophoresis and i get a size of genome around 17 kb. i send the dna to company and sequenced the genome. i got the results but most of blast gave bacterial proteins and one scaffold with a size of 20kb with no hits. so i want to confirm the results i got from company and i want to assemble the bacteriophage and possible annotation. what is the possible course of action i should do? and which software or pipeline i should use? thanks for your help.

[mschmid]

What sequencing technology did you use? Illumina, PacBio or Oxford Nanopore?

[najibveto]

thanks a lot. we used illumina for sequencing.

Answer 1

[Buffo]

Before assembly confirm that you have sequenced a bacteriophage, map your reads to closest-reference, or to bacterial genomes.

[najibveto]

thanks a lot for your advice and sorry for my late reply. should I map the reads to my host bacteria genome or should I download all the bacterial genomes? is there a tutorial for phage assembly or software to do the assembly. thanks a lot.