Alternatives and similar repositories for viral-ngs:

Users that are interested in viral-ngs are comparing it to the libraries listed below

• 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
• sanger-pathogens / circlator
  A tool to circularize genome assemblies
  ☆239Updated 11 months ago
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆355Updated 2 years ago
• wdecoster / nanopack
  An overview of all nanopack tools
  ☆237Updated last year
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆317Updated 9 months ago
• nf-core / viralrecon
  Assembly and intrahost/low-frequency variant calling for viral samples
  ☆133Updated this week
• wdecoster / nanofilt
  Filtering and trimming of long read sequencing data
  ☆201Updated 2 years ago
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆209Updated last year
• schatzlab / genomescope
  Fast genome analysis from unassembled short reads
  ☆284Updated 11 months ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆540Updated 8 months ago
• daler / gffutils
  GFF and GTF file manipulation and interconversion
  ☆297Updated 11 months ago
• ACEnglish / truvari
  Structural variant toolkit for VCFs
  ☆346Updated 3 weeks ago
• rrwick / Filtlong
  quality filtering tool for long reads
  ☆323Updated last year
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆314Updated 3 years ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆208Updated 3 weeks ago
• philres / ngmlr
  NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on r…
  ☆297Updated last year
• AdmiralenOla / Scoary
  Pan-genome wide association studies
  ☆191Updated 9 months ago
• Dfam-consortium / RepeatModeler
  De-Novo Repeat Discovery Tool
  ☆207Updated 2 months ago
• malonge / RaGOO
  RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
  ☆172Updated 3 years ago
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆248Updated 2 weeks ago
• brentp / smoove
  structural variant calling and genotyping with existing tools, but, smoothly.
  ☆248Updated 9 months ago
• fritzsedlazeck / SURVIVOR
  Toolset for SV simulation, comparison and filtering
  ☆374Updated last year
• marbl / SALSA
  SALSA: A tool to scaffold long read assemblies with Hi-C data
  ☆183Updated 10 months ago
• VGP / vgp-assembly
  VGP repository for the genome assembly working group
  ☆190Updated last year
• DRL / blobtools
  Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
  ☆197Updated 7 months ago
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆246Updated last week
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆267Updated last year
• Nextomics / NextPolish
  Fast and accurately polish the genome generated by long reads.
  ☆219Updated 2 months ago
• tseemann / nullarbor
  "Reads to report" for public health and clinical microbiology
  ☆139Updated last year
• ndierckx / NOVOPlasty
  NOVOPlasty - The organelle assembler and heteroplasmy caller
  ☆185Updated last year