Alternatives and similar repositories for vaper

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

• DOH-JDJ0303 / bigbacter-nf
  Bacterial surveillance pipeline.
  ☆26Updated 3 weeks ago
• USDA-VS / GenoFLU
  Influenza data pipeline to automate genotyping assignment
  ☆39Updated 3 months ago
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆32Updated this week
• richardmleggett / MARTi
  Metagenomic Analysis in Real Time
  ☆29Updated 2 months ago
• AMRverse / AMRrules
  Interpretative standards for AMR genotypes
  ☆26Updated last week
• MrTomRod / scoary-2
  Calculate assocations between genes and traits
  ☆29Updated 10 months ago
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆41Updated 2 months ago
• tseemann / cgmlst-dists
  🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
  ☆29Updated 3 weeks ago
• rrwick / Verticall
  Recombination-free trees
  ☆63Updated 4 months ago
• UPHL-BioNGS / Grandeur
  UPHL's Reference Free Pipeline
  ☆27Updated 2 months ago
• GlobalPneumoSeq / gps-pipeline
  Nextflow Pipeline for processing Streptococcus pneumoniae sequencing raw reads (FASTQ files) by the GPS Project (Global Pneumococcal Sequ…
  ☆20Updated 2 weeks ago
• quadram-institute-bioscience / socru
  Order and orientation of complete bacterial genomes
  ☆29Updated 6 months ago
• wslh-bio / spriggan
  Spriggan is a pipeline used for assembly of bacterial whole genome sequence data and identification of antibiotic resistance genes.
  ☆16Updated this week
• bacpop / ggCaller
  Bifrost graph gene caller.
  ☆98Updated last week
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆64Updated 7 months ago
• CFIA-NCFAD / wgscovplot
  The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth informat…
  ☆19Updated last year
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆63Updated last week
• kullrich / snpless-nf
  snpless-nf - A Nextflow pipeline for time-course analysis with bacterial NGS whole-genome data.
  ☆14Updated last year
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆47Updated 3 months ago
• microbinfie-hackathon2020 / CSIS
  Code Safety Inspection Service
  ☆20Updated 3 years ago
• jhuapl-bio / taxtriage
  TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…
  ☆61Updated this week
• CFSAN-Biostatistics / C-WAP
  SC2 variant detection and composition pipeline
  ☆18Updated 2 years ago
• lskatz / fundamentals-of-bioinformatics
  ☆27Updated 8 months ago
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆24Updated 6 years ago
• metagenlab / zDB
  zDB: comparative bacterial genomics made easy
  ☆38Updated last month
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆40Updated 4 months ago
• hoelzer-lab / ribap
  A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
  ☆32Updated last month
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆50Updated 3 years ago
• gtonkinhill / fastbaps
  A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
  ☆68Updated 3 years ago
• boulund / phaster_scripts
  Small utility script to submit genomes to PHASTER for phage detection
  ☆25Updated 4 years ago