Alternatives and similar repositories for SPEAR:

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

• nodrogluap / nanostripper
  Strip reads from Oxford Nanopore FAST5 files if they meet certain criteria
  ☆14Updated 3 years ago
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆28Updated 7 months ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆32Updated 2 months ago
• CDCgov / seqsender
  Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
  ☆34Updated last week
• snake-flu / type_variants
  ☆8Updated 3 years ago
• sanger-pathogens / seroba
  k-mer based Pipeline to identify the Serotype from Illumina NGS reads
  ☆21Updated last year
• CFSAN-Biostatistics / shigatyper
  CFSAN Shigella Typing Pipeline
  ☆14Updated last year
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆25Updated last week
• tseemann / ekidna
  Assembly based core genome SNP alignments for bacteria
  ☆25Updated 5 years ago
• GlobalPathogenAnalysisService / read-it-and-keep
  Read contamination removal
  ☆24Updated last year
• UPHL-BioNGS / Grandeur
  UPHL's Reference Free Pipeline
  ☆25Updated 2 weeks ago
• quick-lab / SARS-CoV-2
  SARs-CoV-2 Primer schemes
  ☆15Updated last year
• mjsull / chromatiblock
  Colinear block visualisation tool
  ☆30Updated last year
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆35Updated 2 months ago
• bacpop / mandrake
  Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
  ☆36Updated this week
• USDA-VS / GenoFLU
  Influenza data pipeline to automate genotyping assignment
  ☆25Updated 2 weeks ago
• CFIA-NCFAD / nf-flu
  Influenza genome analysis Nextflow workflow
  ☆19Updated 3 weeks ago
• treangenlab / Olivar
  Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens
  ☆24Updated 3 weeks ago
• EvolBioInf / phylonium
  ♥ Fast and Accurate Estimation of Evolutionary Distances
  ☆27Updated 9 months ago
• rrwick / Verticall
  Recombination-free trees
  ☆57Updated last year
• simonrharris / SKA
  Split Kmer Analysis
  ☆63Updated 2 years ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆40Updated 4 years ago
• niemasd / ViralConsensus
  Fast viral consensus genome reconstruction
  ☆22Updated 2 months ago
• theiagen / public_health_bacterial_genomics
  ☆27Updated last year
• rpetit3 / fastq-scan
  Output FASTQ summary statistics in JSON format
  ☆29Updated 2 years ago
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆47Updated 3 years ago
• taxprofiler / taxpasta
  TAXnomic Profile Aggregation and STAndardisation
  ☆35Updated 3 months ago
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated 3 months ago
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆26Updated 5 years ago
• SamStudio8 / dehumanizer
  rapidly rid reads of horrid humans
  ☆15Updated 3 years ago