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
• CDCgov / seqsender
  Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
  ☆35Updated last week
• GlobalPathogenAnalysisService / read-it-and-keep
  Read contamination removal
  ☆24Updated last year
• CFIA-NCFAD / nf-flu
  Influenza genome analysis Nextflow workflow
  ☆21Updated last month
• sanger-pathogens / seroba
  k-mer based Pipeline to identify the Serotype from Illumina NGS reads
  ☆21Updated last year
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆26Updated 5 years ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆32Updated 3 months ago
• tseemann / ekidna
  Assembly based core genome SNP alignments for bacteria
  ☆25Updated 5 years ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆41Updated 4 years ago
• rega-cev / virulign
  VIRULIGN: fast codon-correct alignment and annotation of viral genomes
  ☆33Updated 3 years ago
• sanger-pathogens / gff3toembl
  Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
  ☆29Updated 6 years ago
• tseemann / seeka
  Get microbial sequence data easier and faster
  ☆28Updated 5 years ago
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆28Updated 8 months ago
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆37Updated 3 months ago
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated last week
• EvolBioInf / fur
  Find Unique genomic Regions
  ☆29Updated 2 months ago
• josephpetrone / RESCUE
  Resolving Species Level Classification Using Emu
  ☆12Updated 8 months ago
• bacpop / mandrake
  Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
  ☆36Updated this week
• sanger-pathogens / plasmidtron
  Assembling the cause of phenotypes and genotypes from NGS data
  ☆29Updated 4 years ago
• CFSAN-Biostatistics / shigatyper
  CFSAN Shigella Typing Pipeline
  ☆14Updated last year
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆25Updated last month
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆27Updated 2 months ago
• rpetit3 / fastq-scan
  Output FASTQ summary statistics in JSON format
  ☆29Updated 2 years ago
• quick-lab / SARS-CoV-2
  SARs-CoV-2 Primer schemes
  ☆15Updated last year
• rrwick / Verticall
  Recombination-free trees
  ☆57Updated last year
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆19Updated 8 months ago
• SamStudio8 / dehumanizer
  rapidly rid reads of horrid humans
  ☆15Updated 3 years ago
• drpowell / FriPan
  Interactive, web tool for exploring pan-genome of bacterial strains
  ☆45Updated 2 years ago
• tseemann / cgmlst-dists
  🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
  ☆27Updated last year
• UPHL-BioNGS / Grandeur
  UPHL's Reference Free Pipeline
  ☆26Updated last week