Alternatives and similar repositories for bioinfotools

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

• gatk-workflows / gatk4-exome-analysis-pipeline
  This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…
  ☆55Updated 5 years ago
• gatk-workflows / gatk4-somatic-snvs-indels
  This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are al…
  ☆77Updated 5 years ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆98Updated 3 years ago
• broadinstitute / oncotator
  ☆69Updated 3 years ago
• rhshah / IMPACT-Pipeline
  Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
  ☆57Updated 4 years ago
• Jeltje / varscan2
  Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
  ☆30Updated 7 years ago
• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆47Updated 7 years ago
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆72Updated 5 years ago
• gatk-workflows / broad-prod-wgs-germline-snps-indels
  Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad production by https://gi…
  ☆56Updated 5 years ago
• ding-lab / MuSiC2
  identifying mutational significance in cancer genomes
  ☆62Updated 3 years ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆117Updated last year
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated last year
• imgag / ClinCNV
  Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
  ☆91Updated 2 months ago
• bioinfo-pf-curie / TMB
  Tumor Mutational Burden
  ☆63Updated 4 months ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆53Updated last year
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆148Updated 3 months ago
• gatk-workflows / seq-format-conversion
  Workflows for converting between sequence data formats
  ☆39Updated 4 years ago
• likelet / LncPipe
  A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq datasets
  ☆84Updated 3 years ago
• chrisamiller / readDepth
  R package for inferring copy number from read depth
  ☆32Updated 3 years ago
• FoundationMedicineInc / SGZ
  ☆43Updated last year
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆98Updated 4 years ago
• tderrien / FEELnc
  FEELnc : FlExible Extraction of LncRNA
  ☆90Updated 4 months ago
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• 10XGenomics / supernova
  10x Genomics Linked-Read Diploid De Novo Assembler
  ☆65Updated 7 years ago
• RahmanTeam / DECoN
  ☆54Updated 2 years ago
• PubuduSaneth / cnvScan
  CNV screening and annotation tool
  ☆25Updated 9 years ago
• pughlab / ConsensusCruncher
  ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to ama…
  ☆21Updated 3 years ago
• VUmcCGP / wisecondor
  WISECONDOR (WIthin-SamplE COpy Number aberration DetectOR): Detect fetal trisomies and smaller CNV's in a maternal plasma sample using wh…
  ☆47Updated last year
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆75Updated last year
• OpenGene / ctdna-pipeline
  A simplified pipeline for ctDNA sequencing data analysis
  ☆37Updated 8 years ago