Phage Fasta?

[leannmlindsey]

Hello! Thank you for your previous help. I now have a set of prophages identified by Prophage_tracer that I want to further investigate and I want to better understand the output files. I was hoping to find the candidate phages fasta sequence listed somewhere in the output files. The only fasta file that I see in the output is the *.SR.reads.fasta, and from what I can see, I think this is simply the sequence of each of the split reads? Is that correct? So I must use the candidate phage output file locations to cut out the appropriate sequence from the contigs? Would that be the correct way to get the phage sequence?

[WangLab-SCSIO]

Hi, you can install the tool seqkit and use the codeseqkit subseq -r attL_start:attR_end reference.fasta >prophage.fsa to extract the candidate prophage sequence. attL_start and attR_end are the predicted prophage end in the output file. If your are going to deal with many prophages. can the print all the codes in the file and run this file in bash.
'awk 'BEGIN{FS="\t";OFS="\t"} NR>1{print "seqkit subseq -r "$3":"$6" reference.fasta >"$1".fasta"}' strain1.prophage.out >jobfile'
'bash jobfile'

[leannmlindsey]

Thank you so much for this quick reply. I appreciate it.