Alternatives and similar repositories for gffcompare:

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

• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆210Updated this week
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆215Updated last week
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆108Updated 2 years ago
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆147Updated 2 years ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆268Updated 2 months ago
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆247Updated last month
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆157Updated 2 years ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆265Updated last year
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆137Updated 3 years ago
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆273Updated 9 months ago
• kcleal / gw
  Genome browser and variant annotation
  ☆300Updated last week
• wdecoster / nanopack
  An overview of all nanopack tools
  ☆239Updated last year
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆211Updated last year
• epi2me-labs / wf-transcriptomes
  ☆90Updated 3 months ago
• rajewsky-lab / mirdeep2
  Discovering known and novel miRNAs from small RNA sequencing data
  ☆146Updated 7 months ago
• nf-core / nanoseq
  Nanopore demultiplexing, QC and alignment pipeline
  ☆198Updated 2 weeks ago
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆246Updated 2 months ago
• GoekeLab / sg-nex-data
  Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
  ☆127Updated 2 months ago
• BrooksLabUCSC / flair
  Full-Length Alternative Isoform analysis of RNA
  ☆223Updated last week
• mkirsche / Jasmine
  Jasmine: SV Merging Across Samples
  ☆209Updated 3 months ago
• ablab / IsoQuant
  Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
  ☆161Updated this week
• nf-core / fetchngs
  Pipeline to fetch metadata and raw FastQ files from public databases
  ☆174Updated 3 weeks ago
• Nextomics / NextPolish
  Fast and accurately polish the genome generated by long reads.
  ☆220Updated 3 months ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆159Updated 7 months ago
• marbl / SALSA
  SALSA: A tool to scaffold long read assemblies with Hi-C data
  ☆184Updated 10 months ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆235Updated 2 weeks ago
• TransDecoder / TransDecoder
  TransDecoder source
  ☆288Updated 6 months ago
• PacificBiosciences / pbmm2
  A minimap2 frontend for PacBio native data formats
  ☆191Updated last month
• aidenlab / 3d-dna
  3D de novo assembly (3D DNA) pipeline
  ☆208Updated last year
• linsalrob / fastq-pair
  Match up paired end fastq files quickly and efficiently.
  ☆146Updated 10 months ago