Community Q&A: Database of phage genomes for mapping / favorite mapping pipeline?

Here’s a great example of the phage community helping each other out on Twitter — thanks to Stephen Stockdale of APC Microbiome (@SteveStockyPhD) and Simon Roux of the Joint Genome Institute (@simroux_virus) for providing answers!

Here’s the question:

Does anyone know of a database of (putative) phage genomes that you can map reads against? Or your favorite pipeline for mapping reads to a set of references/contigs? Bonus points if it's easy to use for people who don't like coding (that's me)! — @ElysianTweets

The answers (so far):

If you are not comfortable downloading viral RefSeq, there is the complete reference viral database (RVDB) — @SteveStockyPhD

Or Andrew Millard's group @milja001 have an easy to download database — @SteveStockyPhD

Or if you would like easy to download crAss-like phage sequences — @SteveStockyPhD

If you have access to a server that will run alignments and process output (using Bowtie2 and Samtools), but are not comfortable with coding, I can send you some commands. — @SteveStockyPhD

And for mapping reads to genomes without the need to code, we have iVirus on @CyVerseOrg, with full protocols courtesy of Ben Bolduc from @Lab_Sullivan. — @simroux_virus

If you get help from someone in the phage community, or you see an example like this, send it to community@phage.directory — we’d love to feature it here!