Alternatives and similar repositories for nf-flu

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

• BeatsonLab-MicrobialGenomics / micropipe
  A pipeline for high-quality bacterial genome construction using ONT sequencing
  ☆39Updated 2 years ago
• jonas-fuchs / SARS-CoV-2-analyses
  Collection of R scripts for SARS-CoV-2 (variant) analyses
  ☆12Updated 2 years ago
• jonas-fuchs / varVAMP
  Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.
  ☆37Updated 3 weeks ago
• sanger-pathogens / seroba
  k-mer based Pipeline to identify the Serotype from Illumina NGS reads
  ☆24Updated last year
• pauloluniyi / VGEA
  VGEA (Viral Genomes Easily Analyzed) is a pipeline for analysis of RNA virus next-generation sequencing data.
  ☆20Updated 3 years ago
• Serka-M / Digester-MultiSequencing
  Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing
  ☆21Updated 2 years ago
• cmmr / EsViritu
  Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data
  ☆26Updated this week
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆29Updated 11 months ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆37Updated 3 weeks ago
• CFIA-NCFAD / nf-flu
  Influenza genome analysis Nextflow workflow
  ☆22Updated 2 months ago
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 4 years ago
• drboothtj / getphylo
  a python package for automated generation of phylogenetic trees from genbank files
  ☆22Updated 3 months ago
• SegataLab / metamlst
  MetaMLST is a computational tool for in-silico Multi-Locus Sequence Typing from metagenomic data.
  ☆16Updated 2 years ago
• SegataLab / cmseq
  Set of utilities on sequences and BAM files
  ☆27Updated 3 years ago
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆28Updated 2 years ago
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆40Updated last month
• rki-mf1 / clean
  A nextflow pipeline for decontamination of short reads, long reads and contigs
  ☆47Updated 6 months ago
• nf-core / genomeassembler
  Assembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads
  ☆26Updated 2 weeks ago
• marbl / MetaCompass
  MetaCompass: Reference-guided Assembly of Metagenomes
  ☆39Updated last week
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆44Updated 4 years ago
• SWittouck / SCARAP
  A toolkit for prokaryotic comparative genomics
  ☆49Updated 5 months ago
• epi2me-labs / wf-artic
  ARTIC SARS-CoV-2 workflow and reporting
  ☆51Updated 2 months ago
• jonas-fuchs / BAMdash
  create a interactive coverage plot dashboard from bam files and add gb, vcf and bed tracks
  ☆52Updated 2 weeks ago
• EvolBioInf / fur
  Find Unique genomic Regions
  ☆30Updated 2 months ago
• NickJD / ORForise
  Comparison pipeline for Prokaryote Protein Coding Gene Predictors
  ☆23Updated this week
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆27Updated 6 months ago
• tseemann / sixess
  🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files
  ☆24Updated 7 years ago
• biobakery / shortbred
  ShortBRED is a pipeline to take a set of protein sequences, reduce them to a set of unique identifying strings ("markers"), and then sear…
  ☆30Updated 5 months ago
• BackofenLab / CRISPRidentify
  ☆30Updated 5 months ago
• rega-cev / virulign
  VIRULIGN: fast codon-correct alignment and annotation of viral genomes
  ☆35Updated 4 years ago