bactopia
[question] mapping directory
Hello Robert!
I'm having a lot of fun with this pipeline. Right now I'm trying to have bactopia output the mapping files (.bam) too. Thusfar, I hadn't really needed it but I'm trying out a few new tools.
I must be missing something of course. What parameters do I need to provide for bactopia to output and keep the mapping .bam files?
Cheers!
Hi @Svnipni
Glad you are having fun! Are you wanting to get BAM files based alignments to a reference?
Cheers, Robert
Hi Robert! No, preferably aligned to the assembled genome. Amongst other things, I mean to wrap several samples up to construct a pangenome with anvio. If I understand correctly, it needs the .bam file mapped to the fasta and contig.db it constructs.
If you are using Illumina data one thing you could consider is running Snippy with --skip_phylogeny then make use of the BAM files output from Snippy.
Thank you! I tried running snippy before, but it didn't recognize the genbank reference file downloaded from NCBI.
echo "ERROR: Reference file (GCA_012767755.2.gb) does not appear to be a GenBank file"
exit 1
Just for giggles, I tried it with the annotated .gbk.gz output from bactopia but got the same error.
I ran into this issue with snippy. Snippy doesn't like zipped reference files. Unzip the gbk file and it should work.
Should we fix this? In other words, should a compressed Genbank file be an allowed input? (I personally think it should be, and am failing to remember why I didn't allow it.)
Yes, I think it would be good to allow compressed gbk and fna files as inputs.
Hi everyone,
I don't remember when I added it, but the snippy tool will now allow uncompressed and compressed reference files.
Cheers, Robert