Alternatives and similar repositories for FREEC

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

• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆163Updated 2 years ago
• OpenGene / GeneFuse
  Gene fusion detection and visualization
  ☆128Updated 3 years ago
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆147Updated last month
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆137Updated last year
• niu-lab / msisensor2
  Microsatellite instability (MSI) detection for tumor only data.
  ☆110Updated last year
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆193Updated this week
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆143Updated 2 years ago
• genome / breakdancer
  SV detection from paired end reads mapping
  ☆117Updated 6 years ago
• CenterForMedicalGeneticsGhent / WisecondorX
  WisecondorX — An evolved WISECONDOR
  ☆105Updated 2 months ago
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆248Updated last month
• dpryan79 / MethylDackel
  A (mostly) universal methylation extractor for BS-seq experiments.
  ☆172Updated last year
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆109Updated 2 years ago
• ding-lab / msisensor
  microsatellite instability detection using tumor only or paired tumor-normal data
  ☆132Updated 4 years ago
• rajewsky-lab / mirdeep2
  Discovering known and novel miRNAs from small RNA sequencing data
  ☆154Updated last year
• brentp / bwa-meth
  fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
  ☆150Updated 2 months ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆198Updated last year
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆245Updated 3 months ago
• GoekeLab / sg-nex-data
  Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
  ☆141Updated 2 months ago
• Xinglab / rmats2sashimiplot
  ☆153Updated 5 months ago
• broadinstitute / ichorCNA
  Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
  ☆190Updated last year
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆263Updated 2 weeks ago
• CRG-CNAG / CalliNGS-NF
  GATK RNA-Seq Variant Calling in Nextflow
  ☆136Updated 2 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
• bioinform / somaticseq
  An ensemble approach to accurately detect somatic mutations using SomaticSeq
  ☆199Updated 2 months ago
• gatk-workflows / gatk4-germline-snps-indels
  Workflows for germline short variant discovery with GATK4
  ☆138Updated 4 years ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆98Updated 3 years ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆116Updated last year
• tderrien / FEELnc
  FEELnc : FlExible Extraction of LncRNA
  ☆90Updated 3 months ago
• humanlongevity / HLA
  xHLA: Fast and accurate HLA typing from short read sequence data
  ☆113Updated 2 years ago
• zhxiaokang / RASflow
  RNA-Seq analysis workflow
  ☆105Updated 4 years ago