Alternatives and similar repositories for tophat

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

• Tong-Chen / NGS
  Scripts for next generation sequencing
  ☆48Updated 5 years ago
• tderrien / FEELnc
  FEELnc : FlExible Extraction of LncRNA
  ☆87Updated 9 months ago
• aryeelab / guideseq
  Analysis pipeline for the GUIDE-seq assay.
  ☆78Updated 2 years ago
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆58Updated 2 years ago
• ShiLab-Bioinformatics / subread
  The Subread software package is a tool kit for processing next-gen sequencing data. It includes Subread aligner, Subjunc exon-exon juncti…
  ☆45Updated last year
• brentp / bwa-meth
  fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
  ☆149Updated 10 months ago
• rajewsky-lab / mirdeep2
  Discovering known and novel miRNAs from small RNA sequencing data
  ☆148Updated 10 months ago
• MonashBioinformaticsPlatform / RSeQC
  fork of RSeQC python RNAseq metrics suit of tools
  ☆48Updated 6 years ago
• PacificBiosciences / barcoding
  Lima - Demultiplex Barcoded PacBio Samples
  ☆67Updated last month
• LabTranslationalArchitectomics / riboWaltz
  optimization of ribosome P-site positioning in ribosome profiling data
  ☆52Updated 4 months ago
• harbourlab / SparK
  Publication quality NGS track plotting
  ☆113Updated 3 years ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆40Updated 9 years ago
• Zhong-Lab-UCSD / Genomic-Interactive-Visualization-Engine
  Genomic Interactive Visualization Engine
  ☆145Updated 2 years ago
• htseq / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆102Updated 3 weeks ago
• ay-lab / fithic
  Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture…
  ☆86Updated 2 years ago
• tao-bioinfo / gff3sort
  GFF3sort: A Perl Script to sort gff3 files and produce suitable results for tabix tools
  ☆51Updated 5 years ago
• mlbendall / telescope
  Quantification of transposable element expression using RNA-seq
  ☆71Updated last year
• gencorefacility / variant-calling-pipeline-gatk4
  Variant Calling Pipeline Using GATK4 and Nextflow
  ☆56Updated 2 years ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆162Updated 10 months ago
• olarerin / metaPlotR
  A Perl/R pipeline for plotting metagenes
  ☆37Updated 3 years ago
• TrinityCTAT / Trinity_CTAT
  ☆117Updated last year
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆124Updated 2 years ago
• sbslee / fuc
  Frequently used commands in bioinformatics
  ☆57Updated 8 months ago
• smithlabcode / methpipe
  A pipeline for analyzing DNA methylation data from bisulfite sequencing.
  ☆70Updated 2 years ago
• mortazavilab / TranscriptClean
  Correct mismatches, microindels, and noncanonical splice junctions in long reads that have been mapped to the genome
  ☆68Updated last year
• iprada / Circle-Map
  A method for circular DNA detection based on probabilistic mapping of ultrashort reads
  ☆63Updated 11 months ago
• s-andrews / SeqMonk
  SeqMonk NGS visualisation and analysis tool
  ☆49Updated this week
• biocore-ntnu / epic2
  Ultraperformant reimplementation of SICER
  ☆56Updated 3 years ago
• nf-core / hic
  Analysis of Chromosome Conformation Capture data (Hi-C)
  ☆99Updated 3 weeks ago
• ENCODE-DCC / long-rna-seq-pipeline
  STAR based ENCODE Long RNA-Seq processing pipeline
  ☆94Updated 4 years ago