Alternatives and similar repositories for svim:

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

• PacificBiosciences / pbsv
  pbsv - PacBio structural variant (SV) calling and analysis tools
  ☆145Updated 2 months ago
• malonge / RaGOO
  RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
  ☆173Updated 3 years ago
• marbl / SALSA
  SALSA: A tool to scaffold long read assemblies with Hi-C data
  ☆185Updated 11 months ago
• nanoporetech / pipeline-structural-variation
  Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
  ☆114Updated 3 years ago
• mkirsche / Jasmine
  Jasmine: SV Merging Across Samples
  ☆211Updated 4 months ago
• xiaochuanle / NECAT
  Nanopore data assembler
  ☆151Updated 3 years ago
• nanoporetech / pychopper
  A tool to identify, orient, trim and rescue full length cDNA reads
  ☆81Updated 2 years ago
• c-zhou / yahs
  Yet another Hi-C scaffolding tool
  ☆146Updated 6 months ago
• yfukasawa / LongQC
  LongQC is a tool for the data quality control of the PacBio and ONT long reads.
  ☆161Updated last year
• tpoorten / dotPlotly
  Generate an interactive dot plot from mummer or minimap alignments
  ☆200Updated last year
• marcelauliano / MitoHiFi
  Find, circularise and annotate mitogenome from PacBio assemblies
  ☆181Updated 2 months ago
• EichlerLab / pav
  Phased assembly variant caller
  ☆112Updated 5 months ago
• eblerjana / pangenie
  Pangenome-based genome inference
  ☆128Updated 2 weeks ago
• PacificBiosciences / pb-CpG-tools
  Collection of tools for the analysis of CpG data
  ☆81Updated 3 months ago
• bergmanlab / mcclintock
  Meta-pipeline to identify transposable element insertions using next generation sequencing data
  ☆99Updated last year
• KolmogorovLab / Severus
  A tool for somatic structural variant calling using long reads
  ☆128Updated this week
• marbl / ModDotPlot
  ☆145Updated 2 weeks ago
• epi2me-labs / wf-transcriptomes
  ☆91Updated 2 weeks ago
• nanoporetech / rerio
  Research release basecalling models and configurations
  ☆110Updated 10 months ago
• PacificBiosciences / pbmm2
  A minimap2 frontend for PacBio native data formats
  ☆192Updated 2 months ago
• wdecoster / chopper
  ☆185Updated last week
• nanoporetech / pomoxis
  Analysis components from Oxford Nanopore Research
  ☆93Updated 8 months ago
• mahulchak / quickmerge
  A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.
  ☆205Updated 2 years ago
• Nextomics / NextPolish
  Fast and accurately polish the genome generated by long reads.
  ☆222Updated 3 months ago
• informationsea / transanno
  accurate LiftOver tool for new genome assemblies
  ☆124Updated 8 months ago
• dfguan / purge_dups
  haplotypic duplication identification tool
  ☆238Updated last year
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆149Updated 2 years ago
• tangerzhang / ALLHiC
  ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
  ☆176Updated 6 months ago
• wdecoster / cramino
  A *fast* tool for BAM/CRAM quality evaluation, intended for long reads
  ☆149Updated last month
• wdecoster / nanocomp
  Comparison of multiple long read datasets
  ☆127Updated last month