CDCgov / MIRA

Related projects ⓘ

Alternatives and complementary repositories for MIRA

• pha4ge / hAMRonization_workflow
  Harmonization of AMR predictor tool outputs
  ☆21Updated last year
• appliedbinf / pima
  Plasmid and antimicrobial resistance pipeline
  ☆16Updated last year
• CFSAN-Biostatistics / C-WAP
  SC2 variant detection and composition pipeline
  ☆16Updated last year
• tseemann / cgmlst-dists
  🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
  ☆27Updated last year
• UPHL-BioNGS / Grandeur
  UPHL's Reference Free Pipeline
  ☆25Updated 2 weeks ago
• CDCgov / tostadas
  🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission
  ☆27Updated this week
• pha4ge / pha4ge.github.io
  Static website for the PH4AGE alliance
  ☆13Updated last year
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆39Updated 4 years ago
• kullrich / snpless-nf
  snpless-nf - A Nextflow pipeline for time-course analysis with bacterial NGS whole-genome data.
  ☆14Updated 6 months ago
• tseemann / scripts
  Miscellaneous Perl scripts from 20 years in microbial bioinformatics
  ☆16Updated 4 months ago
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆46Updated 2 years ago
• CDCgov / seqsender
  Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
  ☆32Updated this week
• DOH-JDJ0303 / bigbacter-nf
  ☆19Updated last week
• klebgenomics / Kaptive
  ☆44Updated 2 weeks ago
• stjacqrm / centroid
  tool to determine optimal refrerence genome given a set of fasta files
  ☆14Updated last year
• phac-nml / rebar
  REcombination BARcode detector.
  ☆13Updated 7 months ago
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆32Updated last month
• Kalan-Lab / zol
  zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
  ☆49Updated this week
• richardmleggett / MARTi
  Metagenomic Analysis in Real Time
  ☆18Updated last week
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆29Updated last month
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆27Updated 4 months ago
• jonas-fuchs / SARS-CoV-2-analyses
  Collection of R scripts for SARS-CoV-2 (variant) analyses
  ☆12Updated last year
• hoelzer-lab / ribap
  A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
  ☆25Updated 3 weeks ago
• CDCgov / aquascope
  ☆17Updated last week
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆29Updated last month
• tseemann / ekidna
  Assembly based core genome SNP alignments for bacteria
  ☆25Updated 5 years ago
• bacpop / CELEBRIMBOR
  Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs
  ☆22Updated 4 months ago
• MrTomRod / scoary-2
  Calculate assocations between genes and traits
  ☆19Updated 3 weeks ago
• weisberglab / beav
  BEAV: Bacterial Element Annotation reVamped
  ☆59Updated 3 weeks ago
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆52Updated 2 months ago