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
  ☆226Updated 4 months ago
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆162Updated 2 years ago
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆108Updated 2 years ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆244Updated this week
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆282Updated 9 months ago
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆147Updated 10 years ago
• BrooksLabUCSC / flair
  Full-Length Alternative Isoform analysis of RNA
  ☆240Updated this week
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆251Updated last month
• ablab / IsoQuant
  Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
  ☆192Updated last week
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆274Updated 2 years ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆165Updated 2 years ago
• rajewsky-lab / mirdeep2
  Discovering known and novel miRNAs from small RNA sequencing data
  ☆154Updated last year
• GoekeLab / bambu
  Reference-guided transcript discovery and quantification for long read RNA-Seq data
  ☆223Updated last month
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆267Updated last month
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆142Updated 3 months ago
• linsalrob / fastq-pair
  Match up paired end fastq files quickly and efficiently.
  ☆152Updated last year
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆195Updated last week
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆260Updated 2 years ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆172Updated last year
• epi2me-labs / wf-human-variation
  ☆139Updated 2 weeks ago
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆282Updated last week
• nf-core / nanoseq
  Nanopore demultiplexing, QC and alignment pipeline
  ☆214Updated last month
• PacificBiosciences / pbmm2
  A minimap2 frontend for PacBio native data formats
  ☆205Updated this week
• deeptools / HiCExplorer
  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
  ☆256Updated 4 months ago
• mortazavilab / TALON
  Technology agnostic long read analysis pipeline for transcriptomes
  ☆152Updated last year
• alimanfoo / pysamstats
  A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM …
  ☆194Updated 2 weeks ago
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
  ☆180Updated last week
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆249Updated 2 months ago
• GoekeLab / sg-nex-data
  Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
  ☆143Updated 2 months ago
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆284Updated last week