Alternatives and similar repositories for long-read-rna-pipeline

Users that are interested in long-read-rna-pipeline are comparing it to the libraries listed below

• a-slide / NanoCount
  EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
  ☆64Updated last year
• Magdoll / SQANTI2
  SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3
  ☆38Updated 5 years ago
• ENCODE-DCC / wgbs-pipeline
  ENCODE whole-genome bisulfite sequencing (WGBS) pipeline
  ☆32Updated 3 years ago
• WGLab / LIQA
  Long-read Isoform Quantification and Analysis
  ☆38Updated 9 months ago
• Xinglab / espresso
  ☆64Updated 3 months ago
• mortazavilab / TranscriptClean
  Correct mismatches, microindels, and noncanonical splice junctions in long reads that have been mapped to the genome
  ☆70Updated last year
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆61Updated 2 years ago
• adnaniazi / tailfindr
  An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
  ☆55Updated last year
• deepomicslab / SpecHLA
  SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, …
  ☆51Updated 2 months ago
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆75Updated last year
• 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
• ctsa / svtools
  Tools for processing and analyzing structural variants.
  ☆34Updated 10 years ago
• DavidsonGroup / flexiplex
  The Flexible Demultiplexer
  ☆37Updated 3 months ago
• shimlab / BLAZE
  SingleCell Nanopore sequencing data analysis
  ☆62Updated 6 months ago
• AmpliconSuite / CoRAL
  Reconstruction of focal amplifications with long reads
  ☆23Updated last month
• fiberseq / FIRE
  A Snakemake workflow for calling Fiber-seq Inferred Regulatory Elements (FIREs) on single molecules.
  ☆28Updated last month
• parklab / xTea
  Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
  ☆118Updated 5 months ago
• TrinityCTAT / CTAT-LR-fusion
  fusion transcript detection using long reads, leveraging ctat-minimap2 and FusionInspector
  ☆23Updated 2 months ago
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆81Updated 10 months ago
• fritzsedlazeck / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆48Updated 5 years ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆53Updated last year
• smithlabcode / dnmtools
  Tools for analyzing DNA methylation data
  ☆44Updated this week
• khuang28jhu / bs3
  BS-Seeker3: An Ultra-fast, Versatile Pipeline for Mapping Bisulfite-treated Reads.
  ☆29Updated 6 years ago
• cortes-ciriano-lab / savana
  Somatic structural variant caller for long-read data
  ☆86Updated last month
• adamewing / tldr
  Identify and annotate TE-mediated insertions in long-read sequence data
  ☆46Updated 5 months ago
• lh3 / ref-gen
  Human reference genome analysis sets
  ☆56Updated 2 years ago
• tao-bioinfo / gff3sort
  GFF3sort: A Perl Script to sort gff3 files and produce suitable results for tabix tools
  ☆51Updated 5 years ago
• bcgsc / HLAminer
  ⛏ HLA predictions from NGS shotgun data
  ☆55Updated 6 months ago
• bergmanlab / drosophila-transposons
  Drosophila transposable element canonical sequences
  ☆29Updated 3 years ago
• mortazavilab / swan_vis
  A Python library to visualize and analyze long-read transcriptomes
  ☆64Updated 7 months ago