Alternatives and similar repositories for VarSkip:

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

• typhoidgenomics / genotyphi
  Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
  ☆24Updated 5 months ago
• CFSAN-Biostatistics / shigatyper
  CFSAN Shigella Typing Pipeline
  ☆14Updated last year
• andrewjpage / krocus
  Predict MLST directly from uncorrected long reads
  ☆27Updated 3 years ago
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆25Updated last month
• theiagen / public_health_bacterial_genomics
  ☆26Updated last year
• angelovangel / nxf-kraken2
  A simple nextflow pipeline for running kraken2 and bracken in a docker container
  ☆20Updated 4 years ago
• zjshi / Maast
  Microbial agile accurate SNP Typer
  ☆29Updated last year
• rpetit3 / fastq-scan
  Output FASTQ summary statistics in JSON format
  ☆29Updated 2 years ago
• GlobalPathogenAnalysisService / read-it-and-keep
  Read contamination removal
  ☆25Updated last year
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆32Updated 3 months ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆41Updated 4 years ago
• tseemann / ekidna
  Assembly based core genome SNP alignments for bacteria
  ☆25Updated 5 years ago
• mbhall88 / pistis
  Quality control plotting for long reads
  ☆10Updated 10 months ago
• mjsull / chromatiblock
  Colinear block visualisation tool
  ☆30Updated last year
• bacpop / PopPIPE
  Population analysis PIPEline 🛠🧬
  ☆16Updated this week
• kwongj / maskrc-svg
  Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG
  ☆20Updated 6 years ago
• rrwick / Verticall
  Recombination-free trees
  ☆57Updated this week
• lskatz / pdtk
  NCBI Pathogen Detection Portal toolkit
  ☆11Updated last year
• CFIA-NCFAD / nf-flu
  Influenza genome analysis Nextflow workflow
  ☆21Updated this week
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆29Updated 8 months ago
• phiweger / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆15Updated 6 years ago
• B-UMMI / INNUca
  INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search
  ☆15Updated 2 years ago
• nf-core / pathogensurveillance
  Surveillance of pathogens using population genomics and sequencing
  ☆20Updated last week
• lskatz / SneakerNet
  QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run
  ☆11Updated 3 months ago
• jonas-fuchs / SARS-CoV-2-analyses
  Collection of R scripts for SARS-CoV-2 (variant) analyses
  ☆12Updated 2 years ago
• EnzoAndree / FastMLST
  ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies
  ☆24Updated last month
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆57Updated 3 weeks ago
• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆51Updated 3 months ago
• quick-lab / SARS-CoV-2
  SARs-CoV-2 Primer schemes
  ☆15Updated last year
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆39Updated 5 years ago