bacteria
There are 234 repositories under bacteria topic.
oschwengers/bakta
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
Ecogenomics/GTDBTk
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
tseemann/snippy
:scissors: :zap: Rapid haploid variant calling and core genome alignment
labgem/PPanGGOLiN
Build a partitioned pangenome graph from microbial genomes
AdmiralenOla/Scoary
Pan-genome wide association studies
B-UMMI/chewBBACA
BSR-Based Allele Calling Algorithm
tseemann/nullarbor
:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
Pioreactor/pioreactor
Hardware and software for accessible, extensible, and scalable bioreactors. Built on Raspberry Pi.
mgalardini/pyseer
SEER, reimplemented in python 🐍🔮
eead-csic-compbio/get_homologues
GET_HOMOLOGUES: a versatile software package for pan-genome analysis
oschwengers/platon
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
neherlab/pangraph
A bioinformatic toolkit to align genome assemblies into pangenome graphs
bacpop/PopPUNK
PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)
oschwengers/asap
A scalable bacterial genome assembly, annotation and analysis pipeline
cmkobel/CompareM2
🦠🧬🧑💻📇 Microbial genomes-to-report pipeline
kjolley/BIGSdb
Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.
EngqvistLab/Tome
A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima
nf-core/bactmap
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
voorloopnul/awesome-phages
A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.
johnlees/seer
sequence element (kmer) enrichment analysis
karel-brinda/MiniPhy
Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]
karel-brinda/Phylign
Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)
CCB-SB/plsdb
PLSDB pipeline to collect bacterial plasmids from NCBI
prophyle/prophyle
Accurate, resource-frugal and deterministic DNA sequence classifier.
tseemann/phastaf
Identify phage regions in bacterial genomes for masking purposes
Zebbeni/protozoa
A simulation of protozoan behavior and evolution
quadram-institute-bioscience/socru
Order and orientation of complete bacterial genomes
ICBI/viGEN
viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data
ncrna/PathogenTrack
A pipeline to identify pathogenic microorganisms from scRNA-seq raw data.
GunzIvan28/rMAP
Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics using WGS
tseemann/sixess
🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files
oschwengers/tadrep
Targeted Detection and Reconstruction of Plasmids
xthua/bacant
This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.
KThorellGroup/BACTpipe
BACTpipe: An assembly and annotation pipeline for bacterial genomics
mbhall88/NanoVarBench
Evaluating Nanopore-based bacterial variant calling
Danderson123/Amira
A tool to detect acquired AMR genes directly from long read sequencing data.