Alternatives and similar repositories for pima

Users that are interested in pima are comparing it to the libraries listed below

• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆32Updated last week
• janka2012 / digIS
  Pipeline detecting distant and putative novel insertion sequences in prokaryotic genomes
  ☆13Updated 4 years ago
• santirdnd / COPLA
  A taxonomic classifier of plasmids
  ☆28Updated 4 years ago
• LaborBerlin / score-assemblies
  Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).
  ☆26Updated last year
• katholt / reddog-nf
  pipeline for read mapping, snp calling and annotation for bacterial genomes
  ☆13Updated last year
• leaemiliepradier / PlasForest
  A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes
  ☆19Updated 2 years ago
• appliedbinf / el_gato
  ☆10Updated 9 months ago
• wanyuac / GeneMates
  An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences
  ☆27Updated 3 years ago
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆41Updated 2 months ago
• CFSAN-Biostatistics / shigatyper
  CFSAN Shigella Typing Pipeline
  ☆15Updated 2 years ago
• MrTomRod / scoary-2
  Calculate assocations between genes and traits
  ☆29Updated 10 months ago
• kwongj / maskrc-svg
  Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG
  ☆21Updated 6 years ago
• lmc297 / bactaxR
  Bacterial taxonomy construction and evaluation in R
  ☆15Updated last year
• stjacqrm / centroid
  tool to determine optimal refrerence genome given a set of fasta files
  ☆15Updated 2 years ago
• typhoidgenomics / genotyphi
  Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
  ☆28Updated 6 months ago
• katholt / AMRrules
  Organism-specific interpretation of AMR genotypes
  ☆15Updated last year
• metagenlab / zDB
  zDB: comparative bacterial genomics made easy
  ☆38Updated last month
• drpowell / FriPan
  Interactive, web tool for exploring pan-genome of bacterial strains
  ☆48Updated this week
• AMRverse / AMRrules
  Interpretative standards for AMR genotypes
  ☆26Updated this week
• moritzbuck / mOTUlizer
  Utility to analyse a group of closely related MAgs/Genomes/bins/SUBs of more or less dubious origin
  ☆14Updated last year
• wbazant / CORRAL
  ☆14Updated 2 years ago
• quadram-institute-bioscience / socru
  Order and orientation of complete bacterial genomes
  ☆29Updated 6 months ago
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆25Updated 11 months ago
• PROBIC / mGEMS
  mGEMS Genomic epidemiology with mixed samples
  ☆15Updated last year
• erinyoung / roundabout
  Finding regions of similarity between plasmids
  ☆16Updated 3 years ago
• shengzheBian / VPsero
  rapid serotyping of Vibrio parahaemolyticus from whole genome sequencing data using serogroup-specific genes
  ☆10Updated 4 years ago
• ukhsa-collaboration / LOMA
  A Nextflow pipeline designed to classify, align and assemble nanopore metagenomic reads.
  ☆17Updated 10 months ago
• pha4ge / pha4ge.github.io
  Static website for the PH4AGE alliance
  ☆13Updated 2 years ago
• valflanza / accnet
  ☆13Updated 8 years ago
• tseemann / scapper
  Whole genome core alignments from multiple draft genomes
  ☆13Updated 9 years ago