Alternatives and similar repositories for ProblematicSites_SARS-CoV2

Users that are interested in ProblematicSites_SARS-CoV2 are comparing it to the libraries listed below

• pha4ge / pipeline-resources
  Bioinformatics Pipeline and Visualization resources
  ☆55Updated 8 months ago
• jts / ncov-tools
  Small collection of tools for performing quality control on coronavirus sequencing data and genomes
  ☆48Updated last year
• artic-network / primer-schemes
  Primer schemes for real-time genome epidemiology
  ☆27Updated last year
• bede / hostile
  Precise host read removal
  ☆94Updated 3 weeks ago
• epi2me-labs / wf-artic
  ARTIC SARS-CoV-2 workflow and reporting
  ☆51Updated 3 weeks ago
• AllTheBacteria / AllTheBacteria
  Follow up to Grace Blackwell's 661k dataset, for 2023
  ☆102Updated 3 weeks ago
• neherlab / pangraph
  A bioinformatic toolkit to align genome assemblies into pangenome graphs
  ☆103Updated last month
• connor-lab / ncov2019-artic-nf
  A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), wit…
  ☆91Updated last year
• maximilianh / multiSub
  Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input…
  ☆35Updated 3 years ago
• bacpop / PopPUNK
  PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
  ☆97Updated last month
• cov-lineages / pangolin-data
  Repository for storing latest model, protobuf, designation hash and alias files for pangolin assignments
  ☆30Updated last month
• Wytamma / GISAIDR
  Programmatically interact with the GISAID database.
  ☆76Updated last month
• MDU-PHL / abritamr
  A pipeline for running AMRfinderPlus and collating results into functional classes
  ☆78Updated 8 months ago
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆114Updated 11 months ago
• bacpop / ska.rust
  Split k-mer analysis – version 2
  ☆85Updated 3 months ago
• COG-UK / grapevine
  Process consensus file for COG-UK data
  ☆14Updated 3 years ago
• bacpop / ggCaller
  Bifrost graph gene caller.
  ☆94Updated 7 months ago
• virus-evolution / gofasta
  ☆35Updated last month
• CDCgov / datasets-sars-cov-2
  Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)
  ☆54Updated 2 years ago
• gbouras13 / dnaapler
  Reorients assembled microbial sequences
  ☆117Updated last month
• SionBayliss / PIRATE
  A toolbox for pangenome analysis and threshold evaluation.
  ☆97Updated 2 years ago
• INSaFLU / INSaFLU
  INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomi…
  ☆34Updated last month
• simonrharris / SKA
  Split Kmer Analysis
  ☆64Updated 2 years ago
• SamStudio8 / reticulatus
  A snakemake-based pipeline for assembling and polishing long genomes from long nanopore reads
  ☆69Updated 3 years ago
• PoonLab / covizu
  Rapid analysis and visualization of coronavirus genome variation
  ☆48Updated last month
• pathoplexus / pathoplexus
  An open-source pathogen sequence database dedicated to equitable sharing, transparent governance, & empowering global public health.
  ☆36Updated this week
• takaram / kofam_scan
  CLI tool to annotate genes with KOfam
  ☆80Updated last year
• oschwengers / asap
  A scalable bacterial genome assembly, annotation and analysis pipeline
  ☆73Updated last year
• CDCgov / seqsender
  Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
  ☆38Updated last month
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆76Updated 3 years ago