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
  ☆44Updated 2 years ago
• ksahlin / isONcorrect
  Error correction of ONT transcript reads
  ☆59Updated last year
• adnaniazi / tailfindr
  An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
  ☆54Updated 4 months ago
• WGLab / LIQA
  Long-read Isoform Quantification and Analysis
  ☆39Updated last month
• a-slide / NanoCount
  EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
  ☆58Updated 4 months ago
• GeneDx / scramble
  ☆39Updated 9 months ago
• fritzsedlazeck / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆46Updated 4 years ago
• rrazaghi / modbamtools
  Set of tools to manipulate and visualize modified base bam files
  ☆50Updated 2 years ago
• ctsa / svtools
  Tools for processing and analyzing structural variants.
  ☆32Updated 9 years ago
• vaquerizaslab / tadtool
  TADtool is an interactive tool for the identification of meaningful parameters in TAD-calling algorithms for Hi-C data.
  ☆44Updated 2 years ago
• nanoporetech / pipeline-pinfish-analysis
  Pipeline for annotating genomes using long read transcriptomics data with pinfish
  ☆28Updated 4 years ago
• weng-lab / TEMP2
  Algorithm to detect germline and de novo transposon insertions
  ☆27Updated 10 months 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, …
  ☆41Updated last week
• stephenfloor / extract-transcript-regions
  For biological deep sequencing data. Decompose a UCSC knownGenes/Ensembl GTF file into transcript regions (i.e. exons, introns, UTRs and…
  ☆34Updated last year
• PacificBiosciences / barcoding
  Lima - Demultiplex Barcoded PacBio Samples
  ☆65Updated 3 months ago
• epi2me-labs / modbam2bed
  ☆48Updated 5 months ago
• schatzlab / crossstitch
  Code for phasing SVs with SNPs
  ☆52Updated 4 years ago
• PacificBiosciences / sv-benchmark
  Public Benchmark of Long-Read Structural Variant Caller on PacBio CCS HG002 Data
  ☆48Updated 4 years ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆49Updated 6 months ago
• josiegleeson / BamSlam
  Summarise and plot data from long-read ONT (direct RNA/cDNA) BAM files
  ☆13Updated 10 months ago
• adamewing / tldr
  Identify and annotate TE-mediated insertions in long-read sequence data
  ☆41Updated last year
• TomSkelly / MatchAnnot
  Python scripts for matching output of Pacific Biosciences IsoSeq RNA-seq pipeline to an annotation file.
  ☆23Updated 9 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.
  ☆42Updated 7 years ago
• Shians / NanoMethViz
  ☆25Updated 3 weeks ago
• LappalainenLab / lorals
  ☆33Updated last year
• marvin-jens / find_circ
  tools to find circRNAs in RNA-seq data
  ☆42Updated 7 years ago
• nspies / svviz2
  for visual evaluation of read support for structural variation
  ☆51Updated 8 months ago
• cortes-ciriano-lab / savana
  Somatic structural variant caller for long-read data
  ☆57Updated this week
• mortazavilab / swan_vis
  A Python library to visualize and analyze long-read transcriptomes
  ☆58Updated 11 months ago
• mhammell-laboratory / TElocal
  A package for quantifying transposable elements at a locus level for RNAseq datasets.
  ☆24Updated last week