Alternatives and similar repositories for ctDNAtools

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

• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆47Updated 7 years ago
• PapenfussLab / StructuralVariantAnnotation
  R package designed to simplify structural variant analysis
  ☆73Updated 3 years ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆53Updated last year
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆98Updated 4 years ago
• RahmanTeam / DECoN
  ☆54Updated 2 years ago
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆72Updated 5 years ago
• parklab / ShatterSeek
  ☆72Updated 2 years ago
• bcgsc / HLAminer
  ⛏ HLA predictions from NGS shotgun data
  ☆55Updated 6 months ago
• Clinical-Genomics / fusion-report
  Tool for parsing outputs from fusion detection tools. Part of a nf-core/rnafusion pipeline. Checkout a live demo at https://matq007.githu…
  ☆28Updated 5 months ago
• chrisamiller / readDepth
  R package for inferring copy number from read depth
  ☆32Updated 3 years ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 6 years ago
• bioinfo-pf-curie / TMB
  Tumor Mutational Burden
  ☆63Updated 4 months ago
• nf-core / hlatyping
  Precision HLA typing from next-generation sequencing data
  ☆74Updated 2 weeks ago
• stephenfloor / extract-transcript-regions
  For biological deep sequencing data. Decompose a UCSC knownGenes/Ensembl GTF file into transcript regions (i.e. exons, introns, UTRs and…
  ☆36Updated 2 years ago
• Illumina / GTCtoVCF
  Script to convert GTC/BPM files to VCF
  ☆47Updated last month
• hartwigmedical / pipeline5
  ☆21Updated last week
• 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
• Clinical-Genomics / BALSAMIC
  Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
  ☆56Updated last week
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆75Updated last year
• ikalatskaya / ISOWN
  ☆46Updated 6 years ago
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆86Updated 7 years ago
• dieterich-lab / DCC
  DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies …
  ☆37Updated 3 years ago
• Phillip-a-richmond / AnnotateVariants
  This is a pipeline for variant annotation in the diagnosis of rare genetic disorders. It relies on open source data and has instructions …
  ☆18Updated 2 years ago
• dariober / cnv_facets
  Somatic copy variant caller (CNV) for next generation sequencing
  ☆75Updated last year
• saketkc / rna-seq-snakemake
  Snakemake based pipeline for RNA-Seq analysis
  ☆31Updated 6 years ago
• asntech / QDNAseq.hg38
  QDNAseq.hg38: QDNAseq bin annotation for hg38
  ☆17Updated last week
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆99Updated last year
• mhguo1 / TRAPD
  Burden testing against public controls
  ☆50Updated last year
• Jeltje / varscan2
  Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
  ☆30Updated 7 years ago
• naumanjaved / fingerprint_maps
  Create "haplotype maps" of variants in order to use with Picardtools Crosscheck_Files utility, which allows for robust genotyping of func…
  ☆28Updated last year