Alternatives and similar repositories for HiCAssembler:

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

• mskilab-org / gGnome
  R API for browsing, analyzing, and manipulating reference-aligned genome graphs in a GenomicRanges framework
  ☆39Updated last week
• AndreasHeger / gat
  Genomic Association Tester
  ☆30Updated last year
• ay-lab / HiCnv
  HiCnv is used to call copy number variations and breakpoints from Hi-C data
  ☆21Updated 11 months ago
• XiaoTaoWang / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆40Updated 2 years ago
• keleslab / mHiC
  ☆12Updated 4 years ago
• rjdkmr / gcMapExplorer
  Genome Contact Map Explorer - gcMapExplorer. Visit:
  ☆21Updated 3 years ago
• ma-compbio / Phylo-HMRF
  ☆16Updated 4 years ago
• agalitsyna / avTAD
  Plotting average TAD heatmap for Hi-C data (give TAD segmentation and cool/hiclib interactions map).
  ☆10Updated 3 years ago
• TomSkelly / MatchAnnot
  Python scripts for matching output of Pacific Biosciences IsoSeq RNA-seq pipeline to an annotation file.
  ☆23Updated 9 years ago
• parklab / HiNT
  HiC for copy Number variation and Translocation detection
  ☆37Updated 3 years ago
• dixonlab / hic_breakfinder
  ☆36Updated 5 years ago
• czc / nb_distribution
  novoBreak: local assembly for breakpoint detection in cancer genomes
  ☆26Updated 6 years ago
• evotools / nf-LO
  A Nextflow workflow to generate lift over files for any pair of genomes
  ☆56Updated last month
• hall-lab / sv-pipeline
  Pipeline for structural variation detection in cohorts
  ☆49Updated 3 years ago
• keleslab / FreeHiC
  FreeHi-C pipeline for high fidelity Hi-C data simulation.
  ☆11Updated 3 years ago
• adamewing / tldr
  Identify and annotate TE-mediated insertions in long-read sequence data
  ☆41Updated last year
• churchill-lab / g2gtools
  Personal diploid genome creation and coordinate conversion
  ☆24Updated last month
• seqcode / allo
  Allo: a multi-mapped read rescue strategy for gene regulatory analyses
  ☆24Updated 6 months ago
• YingZhou001 / Immuannot
  Immuological gene typing and annotation for genome assembly
  ☆32Updated this week
• cmdoret / hicreppy
  Python reimplementation of hicrep with compatibility for sparse matrices
  ☆17Updated 2 years ago
• Kingsford-Group / rnaseqtools
  toolkit to process gtf files
  ☆17Updated 3 years ago
• XiDsLab / TAGET
  ☆17Updated 2 years ago
• lorrainea / CNEFinder
  CNEFinder: Finding Conserved Non-coding Elements in Genomes
  ☆23Updated 3 years ago
• cortes-ciriano-lab / ReConPlot
  ☆21Updated 3 months ago
• griffithlab / VAtools
  A set of tools to annotate VCF files with expression and readcount data
  ☆29Updated 2 weeks ago
• HenrikBengtsson / TopDom
  R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes
  ☆21Updated last year
• lh3 / etrf
  Exact Tandem Repeat Finder (not a TRF replacement)
  ☆48Updated 5 years ago
• broadinstitute / VariantBam
  Filtering and profiling of next-generational sequencing data using region-specific rules
  ☆25Updated 8 years ago
• jbelyeu / SV-plaudit
  Pipeline for structural variant image curation and analysis.
  ☆48Updated 3 years ago
• ctsa / svtools
  Tools for processing and analyzing structural variants.
  ☆33Updated 9 years ago