Alternatives and similar repositories for SARS-CoV-2

Users that are interested in SARS-CoV-2 are comparing it to the libraries listed below

• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆40Updated 4 months ago
• CDCgov / seqsender
  Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
  ☆38Updated 2 weeks ago
• GuyBaele / SpreadGL
  Main development repository for SpreadGL
  ☆20Updated last year
• nebiolabs / VarSkip
  VarSkip multiplex PCR designs for SARS-CoV-2 sequencing
  ☆14Updated 3 years ago
• rpetit3 / fastq-scan
  Output FASTQ summary statistics in JSON format
  ☆29Updated 3 years ago
• dhelekal / CaveDive
  ☆18Updated last year
• jonas-fuchs / varVAMP
  Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.
  ☆48Updated last week
• nodrogluap / nanostripper
  Strip reads from Oxford Nanopore FAST5 files if they meet certain criteria
  ☆14Updated 4 years ago
• theiagen / public_health_bacterial_genomics
  ☆26Updated 2 years ago
• rrwick / Verticall
  Recombination-free trees
  ☆63Updated 5 months ago
• typhoidgenomics / genotyphi
  Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
  ☆28Updated 6 months ago
• neherlab / pan-genome-visualization
  Visualization of the pan-genome output by panX
  ☆66Updated 7 months ago
• asmngs / asmngs20
  ASMNGS20 - 2020 Conference Details
  ☆15Updated 3 years ago
• theiagen / public_health_viral_genomics
  Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…
  ☆41Updated last year
• jonas-fuchs / SARS-CoV-2-analyses
  Collection of R scripts for SARS-CoV-2 (variant) analyses
  ☆12Updated 2 years ago
• taxprofiler / taxpasta
  TAXnomic Profile Aggregation and STAndardisation
  ☆41Updated 2 months ago
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆59Updated 2 years ago
• sanger-pathogens / seroba
  k-mer based Pipeline to identify the Serotype from Illumina NGS reads
  ☆26Updated 2 years ago
• iqbal-lab-org / viridian
  ☆24Updated 11 months ago
• eclarke / komplexity
  A method of assessing sequence complexity based on kmer frequencies
  ☆33Updated 7 years ago
• treangenlab / Olivar
  Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens
  ☆37Updated 2 weeks ago
• mbhall88 / nohuman
  Remove human reads from a sequencing run
  ☆47Updated last month
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆37Updated last year
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆24Updated 6 years ago
• rega-cev / virulign
  VIRULIGN: fast codon-correct alignment and annotation of viral genomes
  ☆35Updated 4 years ago
• 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…
  ☆36Updated 3 years ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆63Updated 9 months ago
• uio-cels / NucDiff
  In-depth characterization and annotation of differences between two sets of DNA sequences
  ☆63Updated 5 years ago
• pauloluniyi / VGEA
  VGEA (Viral Genomes Easily Analyzed) is a pipeline for analysis of RNA virus next-generation sequencing data.
  ☆20Updated 4 years ago
• cmmr / EsViritu
  Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data
  ☆49Updated last week