Alternatives and similar repositories for long-read-pipelines

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

• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆214Updated last month
• epi2me-labs / wf-transcriptomes
  ☆94Updated 3 weeks ago
• mkirsche / Jasmine
  Jasmine: SV Merging Across Samples
  ☆215Updated 5 months ago
• nanoporetech / pipeline-structural-variation
  Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
  ☆114Updated 3 years ago
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆150Updated 2 years ago
• adamewing / methylartist
  Tools for plotting methylation data in various ways
  ☆151Updated this week
• KolmogorovLab / Severus
  A tool for somatic structural variant calling using long reads
  ☆134Updated last month
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆108Updated 2 years ago
• marbl / SALSA
  SALSA: A tool to scaffold long read assemblies with Hi-C data
  ☆185Updated last year
• PacificBiosciences / pbsv
  pbsv - PacBio structural variant (SV) calling and analysis tools
  ☆149Updated 3 months ago
• nanoporetech / pychopper
  A tool to identify, orient, trim and rescue full length cDNA reads
  ☆82Updated 2 years ago
• biocorecrg / master_of_pores
  Nextflow pipeline for analysis of direct RNA Nanopore reads
  ☆103Updated last month
• parklab / bamsnap
  ☆120Updated 6 months ago
• nf-core / hic
  Analysis of Chromosome Conformation Capture data (Hi-C)
  ☆99Updated this week
• yfukasawa / LongQC
  LongQC is a tool for the data quality control of the PacBio and ONT long reads.
  ☆167Updated last year
• GoekeLab / sg-nex-data
  Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
  ☆129Updated last week
• malonge / RaGOO
  RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
  ☆173Updated 4 years ago
• vibansal / HapCUT2
  software tools for haplotype assembly from sequence data
  ☆218Updated 3 months ago
• cpockrandt / genmap
  GenMap - Fast and Exact Computation of Genome Mappability
  ☆107Updated 11 months ago
• wdecoster / nanocomp
  Comparison of multiple long read datasets
  ☆132Updated 3 weeks ago
• tobiasrausch / alfred
  BAM Statistics, Feature Counting and Annotation
  ☆150Updated 3 months ago
• nanoporetech / rerio
  Research release basecalling models and configurations
  ☆110Updated 2 weeks ago
• bergmanlab / mcclintock
  Meta-pipeline to identify transposable element insertions using next generation sequencing data
  ☆99Updated this week
• ComparativeGenomicsToolkit / hal
  Hierarchical Alignment Format
  ☆168Updated 5 months ago
• hall-lab / svtools
  Tools for processing and analyzing structural variants.
  ☆151Updated 3 years ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆115Updated 10 months ago
• hall-lab / svtyper
  Bayesian genotyper for structural variants
  ☆133Updated 4 years ago
• PacificBiosciences / pbmm2
  A minimap2 frontend for PacBio native data formats
  ☆197Updated 3 months ago
• eblerjana / pangenie
  Pangenome-based genome inference
  ☆127Updated last month
• MariaNattestad / Assemblytics
  Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference gen…
  ☆141Updated 7 months ago