/sytycs

So you think you can species?

Primary LanguageUnrealScriptMIT LicenseMIT

So you think you can (trust your) species (amplicons)?

Prereqs

  • clone this repo
  • set environment variable SYTYCS_CACHEDIR to some location so that genomes can be cached between runs: export SYTYCS_CACHERDIR=$HOME/sytycs_cache
  • a conda env with emboss so we can use primersearch, eg mamba create -n sytycs emboss mafft fasttree vsearch biopython -c conda-forge libiconv

Usage:

Download the desired genus's genomes and run primer search:

bash run.sh Enterococcus AYTGGGYDTAAAGNG CCGTCAATTYHTTTRAGT

Then run the clustering and tree building

bash cluster.sh sytycs_Enterococcus-AYTGGGYDTAAAGNG-CCGTCAATTYHTTTRAGT

V1 Goals:

  • add some ANI-based approach to pre-screen for poor homology that would ruin alignments
  • Swap primersearch for bbmap msa + bbmap extract
  • implement ability to run on higher taxonomic ranks
  • implement subsets
  • switch to infernal for alignment
  • arg to provide outgroup