Alternatives and similar repositories for tophat

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

• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆165Updated 2 years ago
• brentp / bio-playground
  miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.
  ☆182Updated 7 years ago
• ExpressionAnalysis / ea-utils
  Automatically exported from code.google.com/p/ea-utils
  ☆96Updated 2 years ago
• genome / breakdancer
  SV detection from paired end reads mapping
  ☆118Updated 6 years ago
• jstjohn / SeqPrep
  Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
  ☆145Updated 9 years ago
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆354Updated 7 months ago
• simon-anders / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆128Updated 5 years ago
• arq5x / bedtools
  A powerful toolset for genome arithmetic.
  ☆142Updated 4 years ago
• genome / pindel
  Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants …
  ☆174Updated 5 years ago
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆203Updated 4 years ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆201Updated last year
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆173Updated last year
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆148Updated 3 months ago
• ewels / AWS-iGenomes
  Documentation and description of AWS iGenomes S3 resource.
  ☆118Updated last year
• alastair-droop / fqtools
  An efficient FASTQ manipulation suite
  ☆138Updated 5 years ago
• davetang / learning_vcf_file
  Learning the Variant Call Format
  ☆148Updated 4 months ago
• alimanfoo / pysamstats
  A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM …
  ☆195Updated 2 weeks ago
• ENCODE-DCC / kentUtils
  UCSC command line bioinformatic utilities
  ☆187Updated last year
• gatk-workflows / gatk4-somatic-snvs-indels
  This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are al…
  ☆78Updated 5 years ago
• maasha / biopieces
  Biopieces is a bioinformatic framework of tools easily used and easily created.
  ☆144Updated 7 years ago
• dcjones / fastq-tools
  Small utilities for working with fastq sequence files.
  ☆123Updated 3 years ago
• OpenGene / AfterQC
  Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
  ☆212Updated 5 years ago
• CRG-CNAG / CalliNGS-NF
  GATK RNA-Seq Variant Calling in Nextflow
  ☆137Updated 3 years ago
• alyssafrazee / ballgown
  Bioconductor package "ballgown", devel version. Isoform-level differential expression analysis in R.
  ☆148Updated 4 years ago
• PacificBiosciences / DevNet
  The DevNet project on github stores the PacBio DevNet website.
  ☆116Updated 7 years ago
• MikkelSchubert / adapterremoval
  AdapterRemoval v2 - rapid adapter trimming, identification, and read merging
  ☆113Updated 2 weeks ago
• Zhong-Lab-UCSD / Genomic-Interactive-Visualization-Engine
  Genomic Interactive Visualization Engine
  ☆146Updated 2 years ago
• nygenome / lancet
  Microassembly based somatic variant caller for NGS data
  ☆154Updated 3 years ago
• mdshw5 / fastqp
  Simple FASTQ quality assessment using Python
  ☆109Updated 4 years ago
• nh13 / DWGSIM
  Whole Genome Simulator for Next-Generation Sequencing
  ☆102Updated 3 weeks ago