bacteria

There are 4 repositories under bacteria topic.

• tseemann / snippy

  :scissors: :zap: Rapid haploid variant calling and core genome alignment

  variant-callinghaploidbacteriafastq-analysissnpsvcfindel-discoverybioinformaticsgenomics
  Language:Perl 461
• GTDBTk

  Ecogenomics / GTDBTk

  GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

  taxonomyspecies-assignmentsphylogeneticsarchaeabacterianomenclaturebioinformaticsmetagenomics
  Language:Python 460
• bakta

  oschwengers / bakta

  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

  bioinformaticsmicrobial-genomicsgenome-annotationbacteriabacterial-genomesplasmidsmetagenome-assembled-genomesannotationmag
  Language:Python 424
• PPanGGOLiN

  labgem / PPanGGOLiN

  Build a partitioned pangenome graph from microbial genomes

  comparative-genomicsbioinformaticsmicrobial-genomicsmicrobiologybacteriapangenome
  Language:Python 232

• AdmiralenOla / Scoary

  Pan-genome wide association studies

  gene-presence-absencegwaspan-genomebacteriagenomics
  Language:Python 147

• tseemann / nullarbor

  :floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology

  bacteriareportfastqdenovo-assemblyvariant-callinggenotypingresistomevirulomephylogenomicspublic-health
  Language:Perl 133

• B-UMMI / chewBBACA

  BSR-Based Allele Calling Algorithm

  wgmlstcgmlstmlstgenomicsoutbreak-detectionbacterial-genome-analysisallele-callingbioinformaticsbacteriabacterial-typing
  Language:HTML 129

• mgalardini / pyseer

  SEER, reimplemented in python 🐍🔮

  gwasbacteriak-merreimplementationreproducible-science
  Language:Python 108

• eead-csic-compbio / get_homologues

  GET_HOMOLOGUES: a versatile software package for pan-genome analysis

  pangenomebacteriaannotationplantstranscriptomeclusteringfastagenbankpangene
  Language:Perl 104
• platon

  oschwengers / platon

  Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

  microbiologybioinformaticsplasmidsngswgscontigsbacteriaassembly
  Language:Python 104

• Pioreactor / pioreactor

  Hardware and software for accessible, extensible, and scalable bioreactors. Built on Raspberry Pi.

  yeastevolutionbioreactorraspberry-pimqttbiologyraspberrypieducatorsbacteriaalgaehardwaresciencebiotechfermentation
  Language:Python 92

• bacpop / PopPUNK

  PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

  bacteriagenomicspopulation-geneticsk-mersketching
  Language:Python 88

• neherlab / pangraph

  A bioinformatic toolkit to align genome assemblies into pangenome graphs

  bioinformaticsgenomejuliapangraphgenome-assemblypangenomebacteria
  Language:Julia 81
• asap

  oschwengers / asap

  A scalable bacterial genome assembly, annotation and analysis pipeline

  bioinformaticsngsbacteriaassemblyannotationamr
  Language:Groovy 69
• BIGSdb

  kjolley / BIGSdb

  Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.

  bacteriagenomesdatabasemlstbioinformaticstyping
  Language:Perl 56

• cmkobel / CompareM2

  🦠📇 Microbial genomes-to-report pipeline

  microbial-genomicssnakemakegenomes-to-reporthpccondaapptainerbioinformaticspbsslurmbiocondaprokaryotesmetagenomicsclinical-researcharchaeabacteria
  Language:Python 51

• EngqvistLab / Tome

  A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima

  archaeabacteriabioinformaticsenzymeseukaryotesmachine-learningmicrobiologytemperature-data
  Language:Python 51

• nf-core / bactmap

  A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

  bacteriabacterialbacterial-genome-analysisgenomicsmappingnextflownf-corephylogenypipelinetreeworkflow
  Language:Nextflow 50

• voorloopnul / awesome-phages

  A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.

  bacteriabacteriophagesbioinformaticsphages
  43

• johnlees / seer

  sequence element (kmer) enrichment analysis

  gwasbacteriak-mer
  Language:C++ 42

• CCB-SB / plsdb

  PLSDB pipeline to collect bacterial plasmids from NCBI

  plasmidpipelinencbibacteria
  Language:Python 34

• prophyle / prophyle

  Accurate, resource-frugal and deterministic DNA sequence classifier.

  metagenomicsbwtphylogenymetagenomic-classificationbioinformaticsbacteriavirusesburrows-wheeler-transformk-mersphylogenetic-compressionsimplitigsprophyle
  Language:Python 32

• tseemann / phastaf

  Identify phage regions in bacterial genomes for masking purposes

  genomicsbioinformaticsphagebacteria
  Language:Perl 30
• protozoa

  Zebbeni / protozoa

  A simulation of protozoan behavior and evolution

  bacteriaebitenevolutiongolangprotozoaprotozoanssimulationebitenginedecision-treedecision-treessimulations
  Language:Go 28

• ICBI / viGEN

  viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data

  rnaseqvirusbacteriabioinformaticsrgenomicsmetagenomicsviroinformatics
  Language:Shell 26

• ncrna / PathogenTrack

  A pipeline to identify pathogenic microorganisms from scRNA-seq raw data.

  bioinformaticsscrna-seqpathogensbacteriavirusesngsmetagenomicscovid-19
  Language:Python 26

• quadram-institute-bioscience / socru

  Order and orientation of complete bacterial genomes

  bioinformaticspython3bacterialong-readsassemblycompletebioinformatics-pipelineinfectious-diseasesgenomics
  Language:Python 26

• karel-brinda / Phylign

  Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)

  assembliesbacteriabioinformaticscompressiongenomesindexingk-mersmofphylogenetic-compressionphylogeny
  Language:Python 23

• tseemann / sixess

  🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files

  genomicsbacteriaspeciesfastq
  Language:Shell 23

• ctmrbio / BACTpipe

  BACTpipe: An assembly and annotation pipeline for bacterial genomics

  annotationassemblybacteriabioinformaticsnextflowpipelinewhole-genome-sequencing
  Language:Groovy 20
• rMAP

  GunzIvan28 / rMAP

  Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics using WGS

  bacteriaresistomeeskapewgsilluminaphylogenomicsmobilome
  Language:Shell 20

• oschwengers / tadrep

  Targeted Detection and Reconstruction of Plasmids

  bacteriaplasmidswgs
  Language:Python 19

• xthua / bacant

  This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.

  fastaamrintegrontransposonbacteria
  Language:F* 18

• ItzLevvie / Agario-skins

  This project was created from Shell which allows people to download cell skins from https://agar.io.

  agarioagariocellcellsvirusbacteriablobgamegamesweb-gamehtml5funflash
  Language:Shell 16

• karel-brinda / MiniPhy

  Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]

  assembliesbacteriabioinformaticscompressiongenomesindexingk-mersmofphylogenetic-compressionphylogenyprophyle
  Language:Python 14

• DEMENT-Model / DEMENTpy

  A spatially explicit trait- and individual-based microbial systems modelling framework

  dementtraitmicroorganismbacteriafungiindividual-based-modellingenzymeecologycommunity-ecologysoilbiologydementpytrait-based-modellinglitterdecompositiontradeoffmicrobiomefungusgenomeomics
  Language:Python 13