Alternatives and similar repositories for ProblematicSites_SARS-CoV2:

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

• epi2me-labs / wf-artic
  ARTIC SARS-CoV-2 workflow and reporting
  ☆49Updated last month
• artic-network / primer-schemes
  Primer schemes for real-time genome epidemiology
  ☆27Updated last year
• jts / ncov-tools
  Small collection of tools for performing quality control on coronavirus sequencing data and genomes
  ☆48Updated 8 months ago
• 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
• pha4ge / pipeline-resources
  Bioinformatics Pipeline and Visualization resources
  ☆55Updated 4 months ago
• UPHL-BioNGS / Cecret
  Reference-based consensus creation
  ☆51Updated this week
• CDCgov / mycosnp-nf
  CDCgov/mycosnp-nf
  ☆42Updated 3 weeks ago
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆111Updated 7 months ago
• Wytamma / GISAIDR
  Programmatically interact with the GISAID database.
  ☆72Updated 4 months ago
• tseemann / snp-dists
  Pairwise SNP distance matrix from a FASTA sequence alignment
  ☆128Updated 10 months ago
• CDCgov / datasets-sars-cov-2
  Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)
  ☆54Updated last year
• SionBayliss / PIRATE
  A toolbox for pangenome analysis and threshold evaluation.
  ☆92Updated 2 years ago
• neherlab / pangraph
  A bioinformatic toolkit to align genome assemblies into pangenome graphs
  ☆92Updated this week
• 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 2 years ago
• INSaFLU / INSaFLU
  INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomi…
  ☆33Updated last week
• marbl / parsnp
  Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can b…
  ☆132Updated last month
• bacpop / PopPUNK
  PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
  ☆94Updated this week
• pierrebarbera / epa-ng
  Massively parallel phylogenetic placement of genetic sequences
  ☆80Updated 2 years ago
• gbouras13 / hybracter
  Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
  ☆113Updated last month
• MDU-PHL / abritamr
  A pipeline for running AMRfinderPlus and collating results into functional classes
  ☆72Updated 4 months ago
• vgl-hub / gfastats
  A single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulatio…
  ☆96Updated this week
• CFSAN-Biostatistics / C-WAP
  SC2 variant detection and composition pipeline
  ☆16Updated last year
• lskatz / mashtree
  Create a tree using Mash distances
  ☆157Updated last year
• alliblk / genepi-book
  ☆21Updated 6 months ago
• aineniamh / snipit
  snipit: summarise snps relative to your reference sequence
  ☆151Updated 2 months ago
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆43Updated 4 years ago
• replikation / poreCov
  SARS-CoV-2 workflow for nanopore sequence data
  ☆40Updated this week
• takaram / kofam_scan
  CLI tool to annotate genes with KOfam
  ☆73Updated last year
• nf-core / bacass
  Simple bacterial assembly and annotation pipeline
  ☆65Updated 3 weeks ago
• oschwengers / asap
  A scalable bacterial genome assembly, annotation and analysis pipeline
  ☆71Updated last year