Alternatives and similar repositories for hmftools:

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

• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆233Updated 4 months ago
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆266Updated last year
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆243Updated last month
• VanLoo-lab / ascat
  ASCAT R package
  ☆175Updated 2 months ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆248Updated last year
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆156Updated last year
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆182Updated this week
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆262Updated last year
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆207Updated 2 weeks ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆194Updated last year
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆208Updated this week
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆108Updated 2 years ago
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆243Updated last week
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆540Updated 8 months ago
• BrooksLabUCSC / flair
  Full-Length Alternative Isoform analysis of RNA
  ☆220Updated this week
• ENCODE-DCC / rna-seq-pipeline
  ☆147Updated 2 years ago
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆140Updated 2 years ago
• pcingola / SnpEff
  ☆264Updated last month
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆212Updated 8 months ago
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆242Updated 3 months ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆314Updated 3 years ago
• im3sanger / dndscv
  dN/dS methods to quantify selection in cancer and somatic evolution
  ☆220Updated this week
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆157Updated 6 months ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆266Updated last month
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆145Updated last year
• epi2me-labs / wf-transcriptomes
  ☆88Updated 2 months ago
• Illumina / ExpansionHunter
  A tool for estimating repeat sizes
  ☆189Updated last year
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆143Updated last year
• bioinform / somaticseq
  An ensemble approach to accurately detect somatic mutations using SomaticSeq
  ☆197Updated 2 weeks ago
• akdemirlab / HiCPlotter
  “When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau
  ☆183Updated 4 years ago