Alternatives and similar repositories for HiCUP

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

• nf-core / isoseq
  Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed …
  ☆50Updated last month
• BGI-shenzhen / BamDeal
  BamDeal: a comprehensive toolkit for bam manipulation
  ☆54Updated 3 years ago
• vahidAK / NanoMethPhase
  Methylation Phasing for Nanopore Sequencing
  ☆49Updated 2 years ago
• lfaino / LoReAn
  Long Reads Annotation pipeline
  ☆72Updated 3 years ago
• tanghaibao / allhic
  Genome scaffolding based on HiC data in heterozygous and high ploidy genomes
  ☆60Updated last year
• FAANG / analysis-TAGADA
  GENE-SWitCH project RNA-Seq analysis pipeline
  ☆29Updated 10 months ago
• starskyzheng / panpop
  Application of pan-genome for population
  ☆116Updated 2 months ago
• ksahlin / isONcorrect
  Error correction of ONT transcript reads
  ☆58Updated 2 years ago
• shohei-kojima / MEGAnE
  MEGAnE
  ☆33Updated 2 years ago
• nanoporetech / pore-c
  Pore-C support
  ☆53Updated 2 years ago
• ylipacbio / IsoSeq3
  IsoSeq3 - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆19Updated 7 years ago
• drostlab / LTRpred
  De novo annotation of young retrotransposons
  ☆48Updated 3 years ago
• Shians / NanoMethViz
  ☆31Updated 3 months ago
• parklab / xTea
  Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
  ☆118Updated 6 months ago
• bergmanlab / mcclintock
  Meta-pipeline to identify transposable element insertions using next generation sequencing data
  ☆105Updated 7 months ago
• ArimaGenomics / mapping_pipeline
  Mapping pipeline for data generated using Arima-HiC
  ☆81Updated last year
• bergmanlab / drosophila-transposons
  Drosophila transposable element canonical sequences
  ☆29Updated 3 years ago
• phyloacc / PhyloAcc
  PhyloAcc a software to detect the changes of conservation of a genomic region
  ☆34Updated 2 months ago
• bioinfo-chru-strasbourg / vcf2circos
  python plotly Circos from VCF
  ☆40Updated last year
• ENCODE-DCC / long-read-rna-pipeline
  ENCODE long read RNA-seq pipeline
  ☆52Updated 3 years ago
• adamewing / tldr
  Identify and annotate TE-mediated insertions in long-read sequence data
  ☆46Updated 6 months ago
• fritzsedlazeck / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆48Updated 5 years ago
• epi2me-labs / wf-pore-c
  ☆47Updated last month
• Nextomics / pipeline-for-isoseq
  A pipeline for isoseq
  ☆23Updated 7 years ago
• wurmlab / flo
  Same species annotation lift over pipeline.
  ☆98Updated 2 years ago
• pangenome / pggb-workshop
  tutorial on pggb
  ☆36Updated 11 months ago
• xuzhougeng / Genomic_tools
  Genomic related tools
  ☆74Updated 4 years ago
• xuzhougeng / myscripts
  ☆61Updated last year
• PacificBiosciences / HiFiCNV
  Copy number variant caller and depth visualization utility for PacBio HiFi reads
  ☆45Updated last year
• Maggi-Chen / DeBreak
  Structural variant caller for real-time long-read sequencing data
  ☆61Updated 3 years ago