Alternatives and similar repositories for OptiType

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

• bioinform / somaticseq
  An ensemble approach to accurately detect somatic mutations using SomaticSeq
  ☆197Updated 3 weeks ago
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆146Updated 2 years ago
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆137Updated 5 years ago
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆191Updated this week
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
  ☆169Updated this week
• VanLoo-lab / ascat
  ASCAT R package
  ☆186Updated 4 months ago
• oncokb / oncokb-annotator
  Annotates variants in MAF with OncoKB annotation.
  ☆133Updated 3 weeks ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆198Updated last year
• STAR-Fusion / STAR-Fusion
  STAR-Fusion codebase
  ☆243Updated last month
• ENCODE-DCC / rna-seq-pipeline
  ☆153Updated 2 years ago
• broadinstitute / ichorCNA
  Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
  ☆185Updated last year
• virajbdeshpande / AmpliconArchitect
  AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and …
  ☆149Updated last year
• ENCODE-DCC / chip-seq-pipeline
  ENCODE Uniform processing pipeline for ChIP-seq
  ☆123Updated 5 years ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆164Updated 11 months ago
• humanlongevity / HLA
  xHLA: Fast and accurate HLA typing from short read sequence data
  ☆113Updated last year
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆278Updated last year
• kundajelab / chipseq_pipeline
  AQUAS TF and histone ChIP-seq pipeline
  ☆109Updated 3 years ago
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆134Updated last year
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆255Updated 6 months ago
• Xinglab / rmats2sashimiplot
  ☆148Updated 2 months ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆234Updated this week
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆245Updated last week
• WGLab / doc-ANNOVAR
  Documentation for the ANNOVAR software
  ☆243Updated last week
• deeptools / HiCExplorer
  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
  ☆253Updated 2 weeks ago
• griffithlab / pVACtools
  ☆157Updated 3 weeks ago
• Illumina / ExpansionHunter
  A tool for estimating repeat sizes
  ☆195Updated last year
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆237Updated 3 weeks ago
• OpenGene / GeneFuse
  Gene fusion detection and visualization
  ☆128Updated 3 years ago
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆247Updated last month
• sztup / scarHRD
  ☆116Updated last year