Alternatives and similar repositories for nf-flu:

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

• jonas-fuchs / SARS-CoV-2-analyses
  Collection of R scripts for SARS-CoV-2 (variant) analyses
  ☆12Updated 2 years ago
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆29Updated 8 months ago
• theiagen / public_health_bacterial_genomics
  ☆26Updated last year
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆25Updated last month
• andersgs / harrietr
  An `R` package for various phylogenetic and evolutionary biology data manipulations
  ☆12Updated 7 years ago
• CFSAN-Biostatistics / shigatyper
  CFSAN Shigella Typing Pipeline
  ☆14Updated last year
• tseemann / seeka
  Get microbial sequence data easier and faster
  ☆28Updated 5 years ago
• adlape95 / Spaghetti
  Spaghetti: in situ analysis of 16S rRNA amplicons obtained by nanopore sequencing
  ☆15Updated 8 months ago
• 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 / cgmlst-dists
  🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
  ☆27Updated last year
• rega-cev / virulign
  VIRULIGN: fast codon-correct alignment and annotation of viral genomes
  ☆33Updated 3 years ago
• mbhall88 / nohuman
  Remove human reads from a sequencing run
  ☆38Updated 5 months ago
• peterk87 / nf-flu
  Influenza genome analysis Nextflow workflow
  ☆26Updated 2 months ago
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆37Updated 3 months ago
• tseemann / ekidna
  Assembly based core genome SNP alignments for bacteria
  ☆25Updated 5 years ago
• GlobalPathogenAnalysisService / read-it-and-keep
  Read contamination removal
  ☆25Updated last year
• rrwick / Compare-annotations
  A script for comparing old vs new versions of genome annotations
  ☆20Updated last year
• CDCgov / seqsender
  Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
  ☆35Updated 3 weeks ago
• sanger-pathogens / seroba
  k-mer based Pipeline to identify the Serotype from Illumina NGS reads
  ☆21Updated last year
• josephpetrone / RESCUE
  Resolving Species Level Classification Using Emu
  ☆12Updated 9 months ago
• UPHL-BioNGS / Grandeur
  UPHL's Reference Free Pipeline
  ☆26Updated 3 weeks ago
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆39Updated 5 years ago
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆20Updated this week
• colindaven / guppy_on_slurm
  Splitting and accelerating the Oxford Nanopore basecaller guppy using CPU with the SLURM job scheduler
  ☆15Updated 8 months ago
• bacpop / mandrake
  Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
  ☆36Updated 3 weeks ago
• angelovangel / nxf-kraken2
  A simple nextflow pipeline for running kraken2 and bracken in a docker container
  ☆20Updated 4 years ago
• GuyBaele / SpreadGL
  Main development repository for SpreadGL
  ☆18Updated 5 months ago
• lmlui / Jorg
  MAG Circularization Method
  ☆33Updated 2 years ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆41Updated 4 years ago