Alternatives and similar repositories for SQANTI2

Users that are interested in SQANTI2 are comparing it to the libraries listed below

• ENCODE-DCC / long-read-rna-pipeline
  ENCODE long read RNA-seq pipeline
  ☆50Updated 2 years ago
• a-slide / NanoCount
  EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
  ☆61Updated 9 months ago
• TomSkelly / MatchAnnot
  Python scripts for matching output of Pacific Biosciences IsoSeq RNA-seq pipeline to an annotation file.
  ☆23Updated 9 years ago
• ctsa / svtools
  Tools for processing and analyzing structural variants.
  ☆33Updated 9 years ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆50Updated last year
• WGLab / LIQA
  Long-read Isoform Quantification and Analysis
  ☆38Updated 4 months ago
• adamewing / tldr
  Identify and annotate TE-mediated insertions in long-read sequence data
  ☆42Updated last month
• adnaniazi / tailfindr
  An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
  ☆54Updated 9 months ago
• vaquerizaslab / tadtool
  TADtool is an interactive tool for the identification of meaningful parameters in TAD-calling algorithms for Hi-C data.
  ☆47Updated 2 years ago
• deepomicslab / SpecHLA
  SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, …
  ☆46Updated 4 months ago
• fritzsedlazeck / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆48Updated 5 years ago
• shimlab / BLAZE
  SingleCell Nanopore sequencing data analysis
  ☆60Updated 2 months ago
• dixonlab / hic_breakfinder
  ☆36Updated 5 years ago
• josiegleeson / BamSlam
  Summarise and plot data from long-read ONT (direct RNA/cDNA) BAM files
  ☆14Updated last year
• hangelwen / miR-PREFeR
  microRNA PREdiction From small RNA-seq data
  ☆29Updated 7 years ago
• crimBubble / ECCsplorer
  The ECCsplorer is a bioinformatics pipeline for the automated detection of extrachromosomal circular DNA (eccDNA) from paired-end read da…
  ☆20Updated last year
• PapenfussLab / sv_benchmark
  Comprehensive benchmark of structural variant callers
  ☆46Updated 4 years ago
• Xinglab / lr2rmats
  Long read to rMATS
  ☆32Updated 2 years ago
• GeneDx / scramble
  ☆39Updated last year
• TrinityCTAT / CTAT-LR-fusion
  fusion transcript detection using long reads, leveraging ctat-minimap2 and FusionInspector
  ☆22Updated last week
• zyndagj / BSMAPz
  Updated and optimized fork of BSMAP
  ☆22Updated 4 years ago
• DecodeGenetics / svimmer
  Structural variant merging tool
  ☆53Updated 11 months ago
• khuang28jhu / bs3
  BS-Seeker3: An Ultra-fast, Versatile Pipeline for Mapping Bisulfite-treated Reads.
  ☆27Updated 6 years ago
• dnaase / Bis-tools
  A collection of tools to deal with Bisulfite-seq/NOMe-seq (SNP/Methylation calling: BisSNP; HMM segmentation: DMNTools; Visualization/Clu…
  ☆32Updated 3 years ago
• LappalainenLab / lorals
  ☆36Updated 2 years ago
• ksahlin / isONcorrect
  Error correction of ONT transcript reads
  ☆58Updated last year
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆58Updated 2 years ago
• zd1 / telseq
  A software for calculating telomere length
  ☆70Updated 6 years ago
• zhqingit / giremi
  GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data.
  ☆44Updated 8 years ago
• mortazavilab / TranscriptClean
  Correct mismatches, microindels, and noncanonical splice junctions in long reads that have been mapped to the genome
  ☆68Updated last year