Alternatives and similar repositories for public_health_viral_genomics

Users that are interested in public_health_viral_genomics are comparing it to the libraries listed below

• theiagen / public_health_bacterial_genomics
  ☆26Updated 2 years ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆41Updated last week
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆42Updated 4 years ago
• INSaFLU / INSaFLU
  INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomi…
  ☆38Updated 2 weeks ago
• iqbal-lab-org / clockwork
  CRyPTIC data processing pipelines
  ☆34Updated last year
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆45Updated 5 years ago
• pha4ge / pipeline-resources
  Bioinformatics Pipeline and Visualization resources
  ☆58Updated last year
• sanger-pathogens / assembly_improvement
  Improve the quality of a denovo assembly by scaffolding and gap filling
  ☆56Updated 4 years ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆65Updated 3 years ago
• moshi4 / MGCplotter
  Microbial Genome Circular plotting tool for comparative genomics using Circos
  ☆38Updated 2 years ago
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆30Updated last year
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆42Updated 5 years ago
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆51Updated 4 years ago
• sanger-pathogens / plasmidtron
  Assembling the cause of phenotypes and genotypes from NGS data
  ☆29Updated 5 years ago
• dayzerodx / counterr
  ☆31Updated last year
• katholt / RedDog
  ☆37Updated 3 years ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆33Updated 10 months ago
• fmalmeida / MpGAP
  Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
  ☆63Updated last year
• cmmr / EsViritu
  Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data
  ☆42Updated 3 weeks ago
• uio-cels / NucDiff
  In-depth characterization and annotation of differences between two sets of DNA sequences
  ☆63Updated 5 years ago
• CFSAN-Biostatistics / C-WAP
  SC2 variant detection and composition pipeline
  ☆17Updated 2 years ago
• BeatsonLab-MicrobialGenomics / micropipe
  A pipeline for high-quality bacterial genome construction using ONT sequencing
  ☆39Updated 3 years ago
• rki-mf1 / clean
  A nextflow pipeline for decontamination of short reads, long reads and contigs
  ☆55Updated 4 months ago
• Serka-M / Digester-MultiSequencing
  Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing
  ☆21Updated 2 years ago
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆25Updated 6 years ago
• marbl / harvest
  ☆53Updated 4 years ago
• Shamir-Lab / Recycler
  This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye…
  ☆58Updated 4 years ago
• marbl / MetaCompass
  MetaCompass: Reference-guided Assembly of Metagenomes
  ☆39Updated 2 months ago
• theiagen / public_health_bioinformatics
  Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health con…
  ☆56Updated this week
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆41Updated 5 years ago