Alternatives and similar repositories for wf-flu

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

• UPHL-BioNGS / Grandeur
  UPHL's Reference Free Pipeline
  ☆26Updated this week
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 4 years ago
• phac-nml / sistr_cmd
  SISTR (Salmonella In Silico Typing Resource) command-line tool
  ☆27Updated 2 weeks ago
• andrewjpage / krocus
  Predict MLST directly from uncorrected long reads
  ☆27Updated 3 years ago
• scwatts / hicap
  in silico typing of the H. influenzae cap locus
  ☆12Updated 9 months ago
• jonas-fuchs / SARS-CoV-2-analyses
  Collection of R scripts for SARS-CoV-2 (variant) analyses
  ☆12Updated 2 years ago
• CFSAN-Biostatistics / shigatyper
  CFSAN Shigella Typing Pipeline
  ☆14Updated last year
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆25Updated 3 months ago
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆28Updated last week
• jts / assembly_accuracy
  tools for assessing the accuracy of genome assemblies
  ☆34Updated last year
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆51Updated last month
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆59Updated 2 months ago
• xinehc / melon
  Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
  ☆35Updated 2 weeks ago
• Public-Health-Bioinformatics / pubmlst_client
  List and download schemes from pubMLST.org and other BIGSDB servers
  ☆10Updated 6 months ago
• tseemann / cgmlst-dists
  🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
  ☆27Updated last year
• bonsai-team / Porechop_ABI
  Adapter trimmer for Oxford Nanopore reads using ab initio method
  ☆40Updated 5 months ago
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆38Updated last month
• B-UMMI / INNUca
  INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search
  ☆15Updated 2 years ago
• mbhall88 / pistis
  Quality control plotting for long reads
  ☆10Updated 11 months ago
• MigleSur / GenAPI
  Gene Absence Presence Identification tool.
  ☆26Updated last month
• mbhall88 / nohuman
  Remove human reads from a sequencing run
  ☆40Updated 7 months ago
• ukhsa-collaboration / LOMA
  A Nextflow pipeline designed to classify, align and assemble nanopore metagenomic reads.
  ☆13Updated last month
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆33Updated 5 months ago
• hoelzer-lab / ribap
  A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
  ☆27Updated 6 months ago
• UPHL-BioNGS / Donut_Falls
  Basic workflow for nanopore sequencing data
  ☆16Updated 2 weeks ago
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆39Updated 5 years ago
• cmmr / EsViritu
  Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data
  ☆24Updated last year
• CFIA-NCFAD / nf-flu
  Influenza genome analysis Nextflow workflow
  ☆22Updated last month
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated this week
• nickp60 / EzClermont
  Phylotype your strains using Clermont's 2013 method: ezclermont.org
  ☆10Updated 2 years ago