Alternatives and similar repositories for artic-ncov2019:

Users that are interested in artic-ncov2019 are comparing it to the libraries listed below

• aineniamh / snipit
  snipit: summarise snps relative to your reference sequence
  ☆157Updated 2 months ago
• tpoorten / dotPlotly
  Generate an interactive dot plot from mummer or minimap alignments
  ☆199Updated last year
• artic-network / fieldbioinformatics
  The ARTIC field bioinformatics pipeline
  ☆122Updated last week
• 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
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆317Updated 10 months ago
• jtlovell / GENESPACE
  ☆203Updated 2 months ago
• malonge / RaGOO
  RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
  ☆172Updated 3 years ago
• nf-core / viralrecon
  Assembly and intrahost/low-frequency variant calling for viral samples
  ☆134Updated this week
• tseemann / snp-dists
  Pairwise SNP distance matrix from a FASTA sequence alignment
  ☆133Updated last year
• wdecoster / nanofilt
  Filtering and trimming of long read sequencing data
  ☆201Updated 2 years ago
• HKU-BAL / Clair3
  Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
  ☆274Updated this week
• tseemann / nullarbor
  "Reads to report" for public health and clinical microbiology
  ☆139Updated last year
• B-UMMI / chewBBACA
  BSR-Based Allele Calling Algorithm
  ☆141Updated 3 weeks ago
• roblanf / minion_qc
  Quality control for MinION sequencing data
  ☆215Updated 2 years ago
• a-slide / pycoQC
  pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…
  ☆276Updated 5 months ago
• neherlab / pan-genome-analysis
  Processing pipeline for pan-genome visulization and exploration
  ☆138Updated last year
• rrwick / Deepbinner
  a signal-level demultiplexer for Oxford Nanopore reads
  ☆125Updated 4 years ago
• Nextomics / NextPolish
  Fast and accurately polish the genome generated by long reads.
  ☆220Updated 3 months ago
• DRL / blobtools
  Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
  ☆198Updated 7 months ago
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆300Updated this week
• tseemann / mlst
  Scan contig files against PubMLST typing schemes
  ☆221Updated 2 years ago
• wdecoster / chopper
  ☆181Updated 2 weeks ago
• ndierckx / NOVOPlasty
  NOVOPlasty - The organelle assembler and heteroplasmy caller
  ☆186Updated last year
• andersen-lab / ivar
  iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
  ☆120Updated this week
• rrwick / Long-read-assembler-comparison
  Benchmarking of long-read assembly tools for bacterial whole genomes
  ☆170Updated 4 years ago
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆137Updated 3 years ago
• rrwick / Filtlong
  quality filtering tool for long reads
  ☆327Updated last year
• tseemann / shovill
  ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
  ☆222Updated 2 years ago
• mahulchak / quickmerge
  A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.
  ☆204Updated 2 years ago
• tseemann / barrnap
  Bacterial ribosomal RNA predictor
  ☆239Updated last year