Alternatives and similar repositories for nf-flu

Users that are interested in nf-flu are comparing it to the libraries listed below

• theiagen / public_health_bacterial_genomics
  ☆26Updated 2 years ago
• KThorellGroup / BACTpipe
  BACTpipe: An assembly and annotation pipeline for bacterial genomics
  ☆20Updated last year
• jonas-fuchs / SARS-CoV-2-analyses
  Collection of R scripts for SARS-CoV-2 (variant) analyses
  ☆12Updated 2 years ago
• tseemann / ekidna
  Assembly based core genome SNP alignments for bacteria
  ☆25Updated 6 years ago
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆40Updated 4 months ago
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆33Updated last year
• GlobalPathogenAnalysisService / read-it-and-keep
  Read contamination removal
  ☆25Updated 2 years ago
• lskatz / SneakerNet
  QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run
  ☆12Updated last year
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆25Updated 11 months ago
• treangenlab / Olivar
  Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens
  ☆37Updated last week
• andersgs / harrietr
  An `R` package for various phylogenetic and evolutionary biology data manipulations
  ☆12Updated 7 years ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆43Updated 5 years ago
• josephpetrone / RESCUE
  Resolving Species Level Classification Using Emu
  ☆14Updated last year
• adlape95 / Spaghetti
  Spaghetti: in situ analysis of 16S rRNA amplicons obtained by nanopore sequencing
  ☆19Updated last year
• bacpop / mandrake
  Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
  ☆39Updated 10 months ago
• mbhall88 / nohuman
  Remove human reads from a sequencing run
  ☆47Updated last month
• rpetit3 / fastq-scan
  Output FASTQ summary statistics in JSON format
  ☆29Updated 3 years ago
• sanger-pathogens / seroba
  k-mer based Pipeline to identify the Serotype from Illumina NGS reads
  ☆26Updated 2 years ago
• BeatsonLab-MicrobialGenomics / micropipe
  A pipeline for high-quality bacterial genome construction using ONT sequencing
  ☆38Updated 3 years ago
• GuyBaele / SpreadGL
  Main development repository for SpreadGL
  ☆20Updated last year
• janepipistrelle / bacterial_GWAS_tutorial
  Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop
  ☆18Updated 9 years ago
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆24Updated 6 years ago
• jgans / thermonucleotideBLAST
  Searching DNA/RNA sequence databases with PCR and/or probe queries
  ☆23Updated last year
• FOI-Bioinformatics / nanometa_live
  A streamlined workflow and GUI for real-time species identification and pathogen characterization via nanopore sequencing data. Engineere…
  ☆20Updated last year
• taxprofiler / taxpasta
  TAXnomic Profile Aggregation and STAndardisation
  ☆41Updated 2 months ago
• gtonkinhill / pairsnp
  A set of scripts for calculating pairwise SNP distance
  ☆44Updated 3 years ago
• rega-cev / virulign
  VIRULIGN: fast codon-correct alignment and annotation of viral genomes
  ☆35Updated 4 years ago
• kevsilva / StrainFLAIR
  Strain-level abundances estimation in metagenomic samples using variation graphs
  ☆24Updated 3 years ago
• tseemann / seeka
  Get microbial sequence data easier and faster
  ☆28Updated 6 years ago
• phac-nml / biohansel
  Rapidly subtype microbial genomes using single-nucleotide variant (SNV) subtyping schemes
  ☆28Updated last year