Question: bacteriophage genome assembly
gravatar for najibveto
3 months ago by
Korea, Republic Of
najibveto30 wrote:

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.

ADD COMMENTlink modified 3 months ago by Buffo1.1k • written 3 months ago by najibveto30

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

ADD REPLYlink written 3 months ago by mschmid90

thanks a lot. we used illumina for sequencing.

ADD REPLYlink written 5 weeks ago by najibveto30
gravatar for Buffo
3 months ago by
Buffo1.1k wrote:

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

ADD COMMENTlink written 3 months ago by Buffo1.1k

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.

ADD REPLYlink written 5 weeks ago by najibveto30
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