Alternatives and similar repositories for polyploid:

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

• fritzsedlazeck / nibSV
  Kmer based genotyper for short reads.
  ☆23Updated 3 years ago
• kcleal / svbench
  Benchmark structural variant calls against a reference set
  ☆17Updated 5 months ago
• ChaissonLab / hmcnc
  Hidden Markov Model based Copy number caller
  ☆20Updated 5 months ago
• rlorigro / simple-dotplot
  Very simple and configurable all-in-one dotplot program
  ☆12Updated 2 years ago
• hitbc / gcSV
  ☆16Updated last month
• ekg / pafcheck
  PAF (pairwise alignment format) validator based on extended CIGAR strings
  ☆14Updated 6 months ago
• TNTurnerLab / HAT
  HAT is a set of tools for calling de novo variants from whole-genome sequencing data.
  ☆23Updated last year
• DecodeGenetics / LRcaller
  ☆16Updated 3 years ago
• GP2code / CNV-Finder
  Expedite large-scale identification of CNVs within predefined genomic regions. Online app available for those with GP2 Tier 2 Access.
  ☆10Updated 4 months ago
• sinamajidian / phaseme
  A tool set to assess the quality of the per read phasing and reduce the errors.
  ☆12Updated 4 years ago
• mobinasri / secphase
  Phasing reads with secondary alignments
  ☆17Updated 4 months ago
• kehrlab / PopIns2
  Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs
  ☆24Updated 11 months ago
• zeeev / DASVC
  De-novo Assembly Structural Variant Caller
  ☆13Updated 8 years ago
• lh3 / unicall
  A wrapper for calling small variants from human germline high-coverage single-sample Illumina data
  ☆13Updated 5 years ago
• pangenome / vcfbub
  use variant nesting information to flter overlapping sites from vg deconstruct output
  ☆26Updated 9 months ago
• lh3 / minisv
  Lightweight mosaic/somatic SV caller for long reads (WIP)
  ☆28Updated 3 months ago
• luntergroup / bamsplit
  Split a BAM file by haplotype support
  ☆16Updated 7 years ago
• mcfrith / dnarrange
  ☆16Updated 2 months ago
• ComparativeGenomicsToolkit / hal2vg
  Convert HAL to VG
  ☆22Updated 7 months ago
• oscarlr / MsPAC
  Phase reads, assemble haplotypes and detect SVs
  ☆19Updated 4 years ago
• fritzsedlazeck / SVCollector
  Method to optimally select samples for validation and resequencing
  ☆27Updated 3 years ago
• tobiasrausch / lorax
  A long-read analysis toolbox for cancer and population genomics
  ☆22Updated last month
• PacificBiosciences / actc
  Align subreads to ccs reads
  ☆13Updated last year
• ACEnglish / kanpig
  Kmer Analysis of Pileups for Genotyping
  ☆21Updated last month
• LankyCyril / edgecase
  A framework for extracting telomeric reads from single-molecule sequencing experiments, describing their sequence variation and motifs, a…
  ☆16Updated last year
• WHops / NAHRwhals
  R package and wrapper functions for identifying serial structural variations from genome assemblies
  ☆27Updated 6 months ago
• collaborativebioinformatics / GeneVar
  ☆12Updated 3 years ago
• fulcrumgenomics / fgsv
  Tools to gather evidence for structural variation via breakpoint detection.
  ☆19Updated 2 weeks ago
• mchaisso / mcutils
  ☆12Updated 3 years ago
• magspho / hifieval
  a tool to evaluate long-read error correction mainly with PacBio High-Fidelity Reads (HiFi reads).
  ☆21Updated last year