Alternatives and similar repositories for SQANTI

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

• adamewing / tldr
  Identify and annotate TE-mediated insertions in long-read sequence data
  ☆46Updated 5 months ago
• huangnengCSU / longcallR
  LongcallR is a SNP caller for single molecule long-read RNA-seq data
  ☆69Updated this week
• ksahlin / ultra
  Long-read splice alignment with high accuracy
  ☆64Updated last year
• josiegleeson / BamSlam
  Summarise and plot data from long-read ONT (direct RNA/cDNA) BAM files
  ☆15Updated last year
• LappalainenLab / lorals
  ☆38Updated 2 years ago
• mortazavilab / cerberus
  ☆18Updated last year
• KolmogorovLab / minda
  ☆25Updated 7 months ago
• treangenlab / methphaser
  MethPhaser: methylation-based haplotype phasing of human genomes
  ☆51Updated 9 months ago
• Augroup / miniQuant
  Improving gene isoform quantification with miniQuant
  ☆29Updated 2 months ago
• ksahlin / isONcorrect
  Error correction of ONT transcript reads
  ☆58Updated 2 years ago
• a-slide / NanoCount
  EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
  ☆64Updated last year
• schatzlab / crossstitch
  Code for phasing SVs with SNPs
  ☆52Updated 5 years ago
• christopher-vollmers / Mandalorion
  Pipeline to identify isoforms from full-length cDNA sequencing data
  ☆26Updated 2 months ago
• adnaniazi / tailfindr
  An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
  ☆54Updated last year
• fakedrtom / SVAFotate
  ☆44Updated last year
• dixonlab / hic_breakfinder
  ☆37Updated 6 years ago
• zeeev / mergeSVcallers
  heuristics to merge structural variant calls in VCF format.
  ☆38Updated 9 years ago
• Maggi-Chen / FusionSeeker
  A gene fusion caller for long-read transcriptome sequencing data.
  ☆22Updated last year
• cortes-ciriano-lab / ReConPlot
  ☆24Updated 11 months ago
• FAANG / analysis-TAGADA
  GENE-SWitCH project RNA-Seq analysis pipeline
  ☆29Updated 9 months ago
• rrazaghi / modbamtools
  Set of tools to manipulate and visualize modified base bam files
  ☆58Updated 3 years ago
• lh3 / panmask
  Easy genomic regions for short-read variant calling
  ☆45Updated 3 months ago
• HipSTR-Tool / HipSTR
  Genotype and phase short tandem repeats using Illumina whole-genome sequencing data
  ☆32Updated 4 years ago
• multiz / multiz
  DNA multiple sequence aligner, official version from Penn State's Miller Lab
  ☆35Updated 6 years ago
• evotools / nf-LO
  A Nextflow workflow to generate lift over files for any pair of genomes
  ☆69Updated 3 weeks ago
• jonassibbesen / rpvg
  Method for inferring path posterior probabilities and abundances from pangenome graph read alignments
  ☆59Updated 3 months ago
• lh3 / ref-gen
  Human reference genome analysis sets
  ☆56Updated 2 years ago
• mortazavilab / lapa
  Alternative polyadenylation detection from diverse data sources such as 3'-seq, long-read and short-reads.
  ☆31Updated 2 years ago
• seqcode / allo
  Allo: a multi-mapped read rescue strategy for gene regulatory analyses
  ☆24Updated last year
• EichlerLab / smrtsv2
  Structural variant caller
  ☆55Updated 4 years ago