A set of tools for analysing sequence variation around the mcr-1 gene (mobilized colistin resistance).
mcroni takes a fasta file and returns some summary information about the context of mcr-1. It also returns the expected local region for aligning the composite transposon (in progress).
mcroni --fasta genome1.fa --output output_prefix
This will return two output files:
output_prefix_table.tsv : summary information
output_prefix_sequence.fa : extracted sequences
You can also pass in a list of fasta files instead with --filelist:
mcroni --filelist list-of-files.txt --output genomes-output
where list-of-files.txt has the form
path/to/genome1.fa
path/to/genome2.fa
Snesrud et al. (2016) PMID 27620479 proposed a model for the transposition of mcr-1 by ISApl1. A mobile composite transposon structure degraded over time.
Variation within this local genomic context of mcr-1 therefore contains information on its evolutionary history. mcroni doesn't do anything complicated: it's just a convenient wrapper script for assessing this variation automatically (e.g. blasting for ISApl1, finding nearby plasmid replicons).
mcroni assumes there is only one copy of mcr-1 per fasta file. It will give a warning if there are multiple copies. This happens occasionally in real genomes due to the activity of the ISApl1 insertion sequence.
mcroni assumes that contigs are linear. If mcr-1 is near the end of a circularised contig, this could produce incorrect results.
mcroni (pronounced like the pasta).