Alternatives and similar repositories for tools

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

• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆258Updated 2 months ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆543Updated 10 months ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆253Updated last year
• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆201Updated 4 years ago
• nf-core / rnafusion
  RNA-seq analysis pipeline for detection of gene-fusions
  ☆159Updated last week
• ACEnglish / truvari
  Structural variant toolkit for VCFs
  ☆357Updated 3 weeks ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆268Updated last year
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆397Updated this week
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆366Updated this week
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆214Updated last month
• fritzsedlazeck / SURVIVOR
  Toolset for SV simulation, comparison and filtering
  ☆379Updated last year
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆275Updated 11 months ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆317Updated 3 years ago
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆268Updated 2 weeks ago
• brentp / smoove
  structural variant calling and genotyping with existing tools, but, smoothly.
  ☆252Updated 11 months ago
• daler / gffutils
  GFF and GTF file manipulation and interconversion
  ☆299Updated last year
• nf-core / nanoseq
  Nanopore demultiplexing, QC and alignment pipeline
  ☆201Updated last week
• luntergroup / octopus
  Bayesian haplotype-based mutation calling
  ☆311Updated 2 months ago
• bioinform / somaticseq
  An ensemble approach to accurately detect somatic mutations using SomaticSeq
  ☆196Updated last month
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆252Updated 4 months ago
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
  ☆167Updated this week
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆226Updated this week
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆241Updated 2 months ago
• arq5x / lumpy-sv
  lumpy: a general probabilistic framework for structural variant discovery
  ☆327Updated 2 years ago
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆318Updated last week
• GoekeLab / bioinformatics-workflows
  minimal example implementations for bioinformatics workflow managers
  ☆274Updated 3 years ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆341Updated 10 months ago
• nf-core / chipseq
  ChIP-seq peak-calling, QC and differential analysis pipeline.
  ☆215Updated this week
• a-slide / pycoQC
  pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…
  ☆278Updated 7 months ago
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆256Updated 3 weeks ago