Alternatives and similar repositories for local-rearrangements

Users that are interested in local-rearrangements are comparing it to the libraries listed below

• Maize-Genetics-and-Genomics-Database / PanEffect
  PanEffect is a JavaScript framework to explore variant effects across a pangenome. The tool has two views that allows a user to (1) expl…
  ☆13Updated last year
• wjidea / defusion
  defusion
  ☆14Updated 3 years ago
• ekg / fastix
  Prefix-renaming FASTA records really fast.
  ☆17Updated last year
• wtsi-hpag / scaffHiC
  Pipeline for genome scaffolding by modelling distributions of HiC pairs
  ☆9Updated 2 years ago
• njdbickhart / GoatAssemblyScripts
  A loose collection of scripts and utilities for processing and analyzing the Goat reference genome assembly
  ☆11Updated 8 years ago
• SJTU-CGM / PPanG
  a precise pangenome browser combining linear and graph-based pan-genome
  ☆11Updated 11 months ago
• LeilyR / Multi-genome-Reference
  A program to generate a graph which presents a simplified representation of several full length genomes
  ☆13Updated 6 years ago
• fritzsedlazeck / nibSV
  Kmer based genotyper for short reads.
  ☆23Updated 3 years ago
• ASLeonard / pandrawer
  Everything but the kitchen sink
  ☆11Updated 4 months ago
• ekg / pafcheck
  PAF (pairwise alignment format) validator based on extended CIGAR strings
  ☆14Updated 9 months ago
• makovalab-psu / T2T_primate_XY
  ☆12Updated last year
• panlab-bioinfo / RAfilter
  A filter algorithm with program to filter an alignment or mapping file
  ☆10Updated last month
• XuepengSun / apple_diploid_genomes
  ☆10Updated 5 years ago
• mobinasri / secphase
  Phasing reads with secondary alignments
  ☆18Updated 6 months 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 2 weeks ago
• TNTurnerLab / HAT
  HAT is a set of tools for calling de novo variants from whole-genome sequencing data.
  ☆23Updated last year
• T2T-apes / ape_pangenome
  pangenome analyses for complete genomes of great apes (and gibbon)
  ☆17Updated 8 months ago
• StephenHwang / MEMO
  MEMO: MEM-based pangenome indexing for k-mer queries
  ☆18Updated last year
• jnarayan81 / parallelLastz
  parallelLastz: Running Lastz in parallel
  ☆16Updated 9 months ago
• AndreaGuarracino / 1000G-ONT-F100-PGGB
  PanGenome Graph Building with the first 100 assemblies from the 1000G ONT Sequencing Consortium
  ☆12Updated 2 months ago
• jmonlong / manu-vggafannot
  Efficient indexing and querying of annotations in a pangenome graph
  ☆9Updated 2 weeks ago
• LankyCyril / edgecase
  A framework for extracting telomeric reads from single-molecule sequencing experiments, describing their sequence variation and motifs, a…
  ☆16Updated last year
• marbl / training
  Genome Assembly 102
  ☆14Updated 2 months ago
• idanefroni / Conservatory
  Identification of conserved non-coding sequences in plants
  ☆20Updated last month
• ktan8 / nanopore_telomere_basecall
  ☆14Updated last year
• magspho / hifieval
  a tool to evaluate long-read error correction mainly with PacBio High-Fidelity Reads (HiFi reads).
  ☆21Updated last year
• glogsdon1 / sunk-based_assembly
  ☆15Updated 4 years ago
• Walfred-MA / Ctyper
  Genotyping of copy number sensitive allele-specific haplotypes
  ☆15Updated 2 weeks ago
• almeidasilvaf / HybridExpress
  An R package for comparative transcriptomic analyses of hybrids and their progenitors
  ☆14Updated 9 months ago
• gtrichard / mummer-ggplot
  Nucmer from Mummer3 followed by ggplot for nicer and more customisable genome alignment plots.
  ☆11Updated 4 years ago