Alternatives and similar repositories for FREEC

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

• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆143Updated 2 years ago
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆136Updated last year
• OpenGene / GeneFuse
  Gene fusion detection and visualization
  ☆127Updated 3 years ago
• CenterForMedicalGeneticsGhent / WisecondorX
  WisecondorX — An evolved WISECONDOR
  ☆108Updated last week
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆196Updated this week
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆147Updated 2 months ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆165Updated 2 years ago
• gatk-workflows / gatk4-germline-snps-indels
  Workflows for germline short variant discovery with GATK4
  ☆138Updated 4 years ago
• genome / breakdancer
  SV detection from paired end reads mapping
  ☆117Updated 6 years ago
• niu-lab / msisensor2
  Microsatellite instability (MSI) detection for tumor only data.
  ☆112Updated last year
• hall-lab / svtools
  Tools for processing and analyzing structural variants.
  ☆155Updated 3 years ago
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆249Updated 2 months ago
• rajewsky-lab / mirdeep2
  Discovering known and novel miRNAs from small RNA sequencing data
  ☆155Updated last year
• GoekeLab / sg-nex-data
  Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
  ☆145Updated 3 months ago
• lima1 / PureCN
  Copy number calling and variant classification using targeted short read sequencing
  ☆140Updated 3 months ago
• abyzovlab / CNVpytor
  a python extension of CNVnator -- a tool for CNV analysis from depth-of-coverage by mapped reads
  ☆209Updated 2 months ago
• ding-lab / msisensor
  microsatellite instability detection using tumor only or paired tumor-normal data
  ☆132Updated 4 years ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆117Updated last year
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆227Updated 4 months ago
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆108Updated 2 years ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆201Updated last year
• genome / pindel
  Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants …
  ☆174Updated 5 years ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆251Updated 4 months ago
• humanlongevity / HLA
  xHLA: Fast and accurate HLA typing from short read sequence data
  ☆113Updated 2 years ago
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆271Updated last month
• brentp / bwa-meth
  fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
  ☆153Updated 3 months ago
• Ensembl / VEP_plugins
  Plugins for the Ensembl Variant Effect Predictor (VEP)
  ☆162Updated last week
• virajbdeshpande / AmpliconArchitect
  AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and …
  ☆156Updated last year
• broadinstitute / ichorCNA
  Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
  ☆192Updated last year
• tderrien / FEELnc
  FEELnc : FlExible Extraction of LncRNA
  ☆90Updated 4 months ago