Alternatives and similar repositories for easyseq_covid19

Users that are interested in easyseq_covid19 are comparing it to the libraries listed below

• nebiolabs / VarSkip
  VarSkip multiplex PCR designs for SARS-CoV-2 sequencing
  ☆14Updated 3 years ago
• pha4ge / hAMRonization_workflow
  Harmonization of AMR predictor tool outputs
  ☆26Updated 8 months ago
• oma219 / spumoni
  Pan-Genomic Matching Statistics
  ☆54Updated last year
• theiagen / public_health_viral_genomics
  Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…
  ☆41Updated last year
• CDCgov / seqsender
  Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
  ☆38Updated 2 weeks ago
• fmalmeida / MpGAP
  Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
  ☆63Updated last year
• dayzerodx / counterr
  ☆31Updated last year
• 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
• iqbal-lab-org / clockwork
  CRyPTIC data processing pipelines
  ☆34Updated last year
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆38Updated 3 months ago
• SamStudio8 / dehumanizer
  rapidly rid reads of horrid humans
  ☆15Updated 3 years ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆65Updated 3 years ago
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆45Updated 5 years ago
• sirselim / guppy_parameter_optimiser
  A small bash script that automates sweeping Guppy parameters in an attempt to optimise basecalling rate
  ☆30Updated 3 years ago
• nodrogluap / nanostripper
  Strip reads from Oxford Nanopore FAST5 files if they meet certain criteria
  ☆14Updated 4 years ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆41Updated 4 years ago
• broadinstitute / GATK-for-Microbes
  ☆29Updated 3 years ago
• jonas-fuchs / varVAMP
  Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.
  ☆41Updated last month
• asmngs / asmngs20
  ASMNGS20 - 2020 Conference Details
  ☆15Updated 3 years ago
• nf-core / genomeassembler
  Assembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads
  ☆28Updated last month
• theiagen / public_health_bacterial_genomics
  ☆26Updated 2 years ago
• sanger-pathogens / assembly_improvement
  Improve the quality of a denovo assembly by scaffolding and gap filling
  ☆56Updated 4 years ago
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆50Updated 4 years ago
• wdecoster / nanolyse
  Remove lambda phage reads from a fastq file
  ☆29Updated 2 years ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆77Updated 3 years ago
• rrwick / Verticall
  Recombination-free trees
  ☆60Updated last week
• jts / assembly_accuracy
  tools for assessing the accuracy of genome assemblies
  ☆34Updated last year
• cmmr / EsViritu
  Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data
  ☆37Updated 2 weeks ago
• HaploKit / Strainline
  Full-length de novo viral haplotype reconstruction from noisy long reads
  ☆20Updated last year
• pha4ge / pipeline-resources
  Bioinformatics Pipeline and Visualization resources
  ☆57Updated last year