Alternatives and similar repositories for HiCAssembler

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

• ay-lab / HiCnv
  HiCnv is used to call copy number variations and breakpoints from Hi-C data
  ☆21Updated last year
• EI-CoreBioinformatics / portcullis
  Splice junction analysis and filtering from BAM files
  ☆42Updated 3 years ago
• mskilab-org / gGnome
  R API for browsing, analyzing, and manipulating reference-aligned genome graphs in a GenomicRanges framework
  ☆41Updated last week
• hall-lab / sv-pipeline
  Pipeline for structural variation detection in cohorts
  ☆49Updated 4 years ago
• churchill-lab / g2gtools
  Personal diploid genome creation and coordinate conversion
  ☆30Updated 5 months ago
• vaquerizaslab / tadtool
  TADtool is an interactive tool for the identification of meaningful parameters in TAD-calling algorithms for Hi-C data.
  ☆48Updated 2 years ago
• ksahlin / ultra
  Long-read splice alignment with high accuracy
  ☆63Updated 11 months ago
• drostlab / myTAI
  Evolutionary Transcriptomics with R
  ☆45Updated 2 weeks ago
• adamewing / tldr
  Identify and annotate TE-mediated insertions in long-read sequence data
  ☆42Updated 2 months ago
• AndreasHeger / gat
  Genomic Association Tester
  ☆32Updated 2 years ago
• TomSkelly / MatchAnnot
  Python scripts for matching output of Pacific Biosciences IsoSeq RNA-seq pipeline to an annotation file.
  ☆23Updated 9 years ago
• dixonlab / hic_breakfinder
  ☆37Updated 6 years ago
• rjdkmr / gcMapExplorer
  Genome Contact Map Explorer - gcMapExplorer. Visit:
  ☆21Updated 3 years ago
• VCCRI / SVPV
  Structural Variant Prediction Viewer
  ☆35Updated 8 years ago
• XiDsLab / TAGET
  ☆19Updated 2 years ago
• Magdoll / SQANTI2
  SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3
  ☆38Updated 5 years ago
• BlanchetteLab / HIFI
  Hi-C Interaction Frequency Inference (HIFI): High-resolution estimation of DNA-DNA interaction frequency from Hi-C data
  ☆24Updated 2 years ago
• cortes-ciriano-lab / ReConPlot
  ☆23Updated 9 months ago
• LappalainenLab / lorals
  ☆36Updated 2 years ago
• seqcode / allo
  Allo: a multi-mapped read rescue strategy for gene regulatory analyses
  ☆24Updated last year
• deeptools / HiCBrowser
  Simple web browser to visualize HiC tracks
  ☆18Updated 5 years ago
• adnaniazi / tailfindr
  An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
  ☆54Updated 11 months ago
• sanjaynagi / rna-seq-pop
  Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data
  ☆18Updated 5 months ago
• dellytools / sansa
  Structural variant VCF annotation, duplicate removal and comparison
  ☆33Updated 6 months ago
• brwnj / covviz
  Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata
  ☆58Updated 3 years ago
• TheJacksonLaboratory / SVE
  ☆51Updated 6 years ago
• keleslab / mHiC
  ☆12Updated 5 years ago
• zeeev / mergeSVcallers
  heuristics to merge structural variant calls in VCF format.
  ☆36Updated 8 years ago
• czc / nb_distribution
  novoBreak: local assembly for breakpoint detection in cancer genomes
  ☆25Updated 7 years ago
• stephenturner / adapters
  Adapters for trimming
  ☆30Updated 6 years ago