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
• CenterForMedicalGeneticsGhent / WisecondorX
  WisecondorX — An evolved WISECONDOR
  ☆103Updated last month
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆137Updated last year
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆163Updated 2 years ago
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆147Updated 3 weeks ago
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆194Updated this week
• niu-lab / msisensor2
  Microsatellite instability (MSI) detection for tumor only data.
  ☆110Updated last year
• OpenGene / GeneFuse
  Gene fusion detection and visualization
  ☆128Updated 3 years ago
• genome / breakdancer
  SV detection from paired end reads mapping
  ☆117Updated 6 years ago
• rajewsky-lab / mirdeep2
  Discovering known and novel miRNAs from small RNA sequencing data
  ☆154Updated last year
• ding-lab / msisensor
  microsatellite instability detection using tumor only or paired tumor-normal data
  ☆132Updated 4 years ago
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆246Updated 2 weeks ago
• lima1 / PureCN
  Copy number calling and variant classification using targeted short read sequencing
  ☆140Updated last month
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆223Updated 2 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
• brentp / bwa-meth
  fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
  ☆150Updated last month
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆263Updated last week
• AstraZeneca-NGS / VarDict
  VarDict
  ☆198Updated last year
• GoekeLab / sg-nex-data
  Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
  ☆138Updated last month
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆116Updated last year
• bioinform / somaticseq
  An ensemble approach to accurately detect somatic mutations using SomaticSeq
  ☆199Updated 2 months ago
• genome / pindel
  Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants …
  ☆174Updated 5 years ago
• hall-lab / svtools
  Tools for processing and analyzing structural variants.
  ☆154Updated 3 years ago
• mortazavilab / TALON
  Technology agnostic long read analysis pipeline for transcriptomes
  ☆151Updated last year
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆158Updated 2 years ago
• VanLoo-lab / ascat
  ASCAT R package
  ☆189Updated 2 weeks ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆242Updated 2 months ago
• abyzovlab / CNVnator
  a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
  ☆228Updated 3 years ago
• tobiasrausch / alfred
  BAM Statistics, Feature Counting and Annotation
  ☆150Updated this week
• abyzovlab / CNVpytor
  a python extension of CNVnator -- a tool for CNV analysis from depth-of-coverage by mapped reads
  ☆205Updated this week