ProphagePredictionComparisons

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Hello, I wanted to test your compare_predictions_to_phages.py to make sure that it was working, so I used the tsv file containing the reference locations for phages in NC_002655. I was...

leannmlindsey

Some contig accession numbers in the Supplementary Tables seem to be incorrect?

2

I tried to download all of the genomes using the "Contig accession" column in the supplementary table and these are the ones that were not recognized: 411479.31.con.0020 1351.557.con.0001 1280.10152.con.0001 Searching...

leannmlindsey

https://github.com/chg60/DEPhT

beardymcjohnface

[Suggestion] Add strand information to the gbk files

1

Gene strand can be very useful to detect prophages, but it is currently lacking from the `.gb` files. Because of that, there's no way to benchmark a tool that leverages...

apcamargo

Hey Rob, The *Paracoccus sanguinis* 5503 genome has a couple of duplicated protein IDs, which can cause troubles in downstream analysis. Here's the list: ``` WP_036707377.1 WP_036703025.1 WP_036705789.1 WP_036712647.1 WP_036705789.1...

apcamargo

Hey Rob! The *Escherichia coli* K12 genome seems to be missing more than one prophage. Here's one that I curated manually: ``` contig gene start end --------------------------------------------------------------- NC_000913 RAST2:fig|83333.998.peg.2428 2464528...

apcamargo

Request to add tool and other thoughts

2

Hi Rob, I was really excited to see that someone is doing a comparison of different prophage tools. If you are still open to adding more tools for comparison, I...

mtisza1