Alternatives and similar repositories for strelka

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

• WGLab / doc-ANNOVAR
  Documentation for the ANNOVAR software
  ☆242Updated 2 months ago
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆470Updated last month
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆317Updated 3 years ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆543Updated 10 months ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆241Updated 2 months ago
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆318Updated last week
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆432Updated last year
• nservant / HiC-Pro
  HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
  ☆406Updated last year
• abyzovlab / CNVnator
  a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
  ☆222Updated 3 years ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆200Updated last year
• deeptools / HiCExplorer
  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
  ☆249Updated 6 months ago
• dpryan79 / ChromosomeMappings
  This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
  ☆241Updated 2 years ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆159Updated 2 years ago
• pcingola / SnpEff
  ☆277Updated 3 months ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆253Updated last year
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆366Updated this week
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆268Updated last year
• adamewing / bamsurgeon
  tools for adding mutations to existing .bam files, used for testing mutation callers
  ☆241Updated 7 months ago
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆442Updated last year
• shenlab-sinai / ngsplot
  Quick mining and visualization of NGS data by integrating genomic databases
  ☆265Updated 2 years ago
• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆201Updated 3 weeks ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆270Updated 4 months ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆230Updated 4 years ago
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆268Updated 2 weeks ago
• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆201Updated 4 years ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆224Updated last week
• philres / ngmlr
  NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on r…
  ☆301Updated last year
• agshumate / Liftoff
  An accurate GFF3/GTF lift over pipeline
  ☆482Updated last year
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆295Updated 2 years ago
• Illumina / manta
  Structural variant and indel caller for mapped sequencing data
  ☆429Updated 2 years ago