Alternatives and similar repositories for gffcompare

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

• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆251Updated last week
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆227Updated 6 months ago
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆167Updated 2 years ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆284Updated 11 months ago
• BrooksLabUCSC / flair
  Full-Length Alternative Isoform analysis of RNA
  ☆246Updated this week
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆108Updated 2 years ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆278Updated 2 years ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆257Updated 3 months ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆165Updated 2 years ago
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆148Updated 10 years ago
• ablab / IsoQuant
  Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
  ☆198Updated last week
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆279Updated 3 months ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆262Updated 2 years ago
• rajewsky-lab / mirdeep2
  Discovering known and novel miRNAs from small RNA sequencing data
  ☆158Updated 3 weeks ago
• wdecoster / nanopack
  An overview of all nanopack tools
  ☆274Updated 2 years ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆175Updated last year
• nf-core / nanoseq
  Nanopore demultiplexing, QC and alignment pipeline
  ☆218Updated last month
• alimanfoo / pysamstats
  A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM …
  ☆195Updated last week
• BGI-shenzhen / LDBlockShow
  LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files
  ☆198Updated 6 months ago
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆274Updated 2 months ago
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆200Updated this week
• mortazavilab / TALON
  Technology agnostic long read analysis pipeline for transcriptomes
  ☆154Updated last year
• GoekeLab / bambu
  Reference-guided transcript discovery and quantification for long read RNA-Seq data
  ☆223Updated this week
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆217Updated 2 years ago
• linsalrob / fastq-pair
  Match up paired end fastq files quickly and efficiently.
  ☆153Updated last year
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆143Updated 5 months ago
• abyzovlab / CNVnator
  a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
  ☆232Updated 3 years ago
• WGLab / doc-ANNOVAR
  Documentation for the ANNOVAR software
  ☆245Updated 5 months ago
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair
  ☆185Updated 3 weeks ago
• deeptools / HiCExplorer
  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
  ☆262Updated 5 months ago