bacteria topic
GTDBTk
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
bakta
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
PPanGGOLiN
Build a partitioned pangenome graph from microbial genomes
snippy
:scissors: :zap: Rapid haploid variant calling and core genome alignment
nullarbor
:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
Scoary
Pan-genome wide association studies
platon
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
get_homologues
GET_HOMOLOGUES: a versatile software package for pan-genome analysis
PopPUNK
PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)
pyseer
SEER, reimplemented in python 🐍🔮