Alternatives and similar repositories for pepper:

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

• HKU-BAL / Clair3
  Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
  ☆265Updated last week
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆266Updated last month
• isovic / racon
  Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr…
  ☆278Updated 10 months ago
• Nextomics / NextPolish
  Fast and accurately polish the genome generated by long reads.
  ☆218Updated 2 months ago
• mkirsche / Jasmine
  Jasmine: SV Merging Across Samples
  ☆207Updated 2 months ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆207Updated 2 weeks ago
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆143Updated last year
• a-slide / pycoQC
  pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…
  ☆276Updated 4 months ago
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆136Updated 3 years ago
• wdecoster / nanopack
  An overview of all nanopack tools
  ☆236Updated last year
• nanoporetech / ont_fast5_api
  Oxford Nanopore Technologies fast5 API software
  ☆152Updated last year
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆182Updated this week
• yfukasawa / LongQC
  LongQC is a tool for the data quality control of the PacBio and ONT long reads.
  ☆159Updated last year
• ACEnglish / truvari
  Structural variant toolkit for VCFs
  ☆342Updated last week
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆299Updated 3 weeks ago
• brentp / smoove
  structural variant calling and genotyping with existing tools, but, smoothly.
  ☆248Updated 8 months ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆212Updated 8 months ago
• marbl / SALSA
  SALSA: A tool to scaffold long read assemblies with Hi-C data
  ☆183Updated 9 months ago
• lbcb-sci / racon
  Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads
  ☆214Updated last year
• sanger-pathogens / circlator
  A tool to circularize genome assemblies
  ☆238Updated 11 months ago
• nanoporetech / pipeline-structural-variation
  Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
  ☆114Updated 3 years ago
• nanoporetech / pychopper
  A tool to identify, orient, trim and rescue full length cDNA reads
  ☆81Updated 2 years ago
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆247Updated 4 months ago
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆266Updated last year
• malonge / RaGOO
  RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
  ☆172Updated 3 years ago
• PacificBiosciences / pbmm2
  A minimap2 frontend for PacBio native data formats
  ☆186Updated 2 weeks ago
• fritzsedlazeck / SURVIVOR
  Toolset for SV simulation, comparison and filtering
  ☆373Updated last year
• novoalab / EpiNano
  Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)
  ☆113Updated 8 months ago
• nanoporetech / taiyaki
  Training models for basecalling Oxford Nanopore reads
  ☆115Updated 3 years ago
• rrwick / Deepbinner
  a signal-level demultiplexer for Oxford Nanopore reads
  ☆124Updated 4 years ago