Alternatives and similar repositories for pangene:

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

• huangnengCSU / compleasm
  A genome completeness evaluation tool based on miniprot
  ☆195Updated last week
• eblerjana / pangenie
  Pangenome-based genome inference
  ☆127Updated last week
• wdecoster / chopper
  ☆178Updated last month
• bergmanlab / mcclintock
  Meta-pipeline to identify transposable element insertions using next generation sequencing data
  ☆96Updated last year
• PacificBiosciences / trgt
  Tandem repeat genotyping and visualization from PacBio HiFi data
  ☆114Updated last month
• moiexpositoalonsolab / grenepipe
  A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles - fo…
  ☆95Updated 3 weeks ago
• tobiasrausch / wally
  Wally: Visualization of aligned sequencing reads and contigs
  ☆113Updated 3 months ago
• wdecoster / cramino
  A *fast* tool for BAM/CRAM quality evaluation, intended for long reads
  ☆142Updated last week
• EichlerLab / pav
  Phased assembly variant caller
  ☆111Updated 3 months ago
• PacificBiosciences / pb-CpG-tools
  Collection of tools for the analysis of CpG data
  ☆80Updated last month
• EVidenceModeler / EVidenceModeler
  source code for EVM
  ☆109Updated 3 months ago
• mkirsche / Jasmine
  Jasmine: SV Merging Across Samples
  ☆208Updated 3 months ago
• colindaven / awesome-pangenomes
  A list of software for pangenomics
  ☆106Updated 2 weeks ago
• cgroza / GraffiTE
  GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered …
  ☆173Updated this week
• tolkit / telomeric-identifier
  Identify and find telomeres, or telomeric repeats in a genome.
  ☆123Updated 2 weeks ago
• zhangrengang / TEsorter
  TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes
  ☆92Updated last month
• marschall-lab / panacus
  Panacus is a tool for computing statistics for GFA-formatted pangenome graphs
  ☆99Updated this week
• marcelauliano / MitoHiFi
  Find, circularise and annotate mitogenome from PacBio assemblies
  ☆176Updated 2 weeks ago
• ncbi / egapx
  Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation
  ☆118Updated 2 months ago
• yfukasawa / LongQC
  LongQC is a tool for the data quality control of the PacBio and ONT long reads.
  ☆159Updated last year
• Dfam-consortium / TETools
  Dfam Transposable Element Tools Docker container.
  ☆88Updated last week
• xiaochuanle / NECAT
  Nanopore data assembler
  ☆146Updated 2 years ago
• DessimozLab / read2tree
  a tool for inferring species tree from sequencing reads
  ☆146Updated last month
• informationsea / transanno
  accurate LiftOver tool for new genome assemblies
  ☆124Updated 7 months ago
• hahnlab / CAFE5
  Version 5 of the CAFE phylogenetics software
  ☆129Updated last month
• CSU-KangHu / HiTE
  High-precision TE Annotator
  ☆103Updated 2 weeks ago
• nanoporetech / rerio
  Research release basecalling models and configurations
  ☆107Updated 9 months ago
• twolinin / longphase
  ☆109Updated 2 weeks ago
• aaranyue / quarTeT
  A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification
  ☆125Updated this week
• sheinasim-USDA / HiFiAdapterFilt
  Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz).
  ☆86Updated 8 months ago