Alternatives and similar repositories for PyLOH

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

• getzlab / deTiN
  DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…
  ☆53Updated 3 years ago
• Ettwiller / Damage-estimator
  Estimate damage in standard NGS library preparation. Incompatible with library preparation methods from which the imbalance is lost (such…
  ☆54Updated 8 years ago
• chrisamiller / readDepth
  R package for inferring copy number from read depth
  ☆32Updated 3 years ago
• walaj / VariantBam
  Filtering and profiling of next-generational sequencing data using region-specific rules
  ☆79Updated 2 years ago
• sfu-compbio / sinvict
  SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA
  ☆27Updated 5 years ago
• nygenome / Conpair
  Concordance and contamination estimator for tumor–normal pairs
  ☆58Updated last year
• slzhao / QC3
  QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.
  ☆32Updated 9 years ago
• ctsa / svtools
  Tools for processing and analyzing structural variants.
  ☆34Updated 10 years ago
• macarthur-lab / igv_utils
  utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.
  ☆49Updated 6 years ago
• dantaki / SV2
  Support Vector Structural Variation Genotyper
  ☆58Updated 5 years ago
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆80Updated 9 months ago
• deaconjs / ThousandVariantCallersRepo
  Thousand Variant Callers Project Repository
  ☆74Updated 6 years ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆99Updated 3 years ago
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• TheJacksonLaboratory / SVE
  ☆51Updated 6 years ago
• ikalatskaya / ISOWN
  ☆46Updated 6 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
• tk2 / RetroSeq
  RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference…
  ☆67Updated 3 years ago
• bcbio / bcbio_validations
  Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses
  ☆31Updated 3 years ago
• Magdoll / SQANTI2
  SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3
  ☆38Updated 5 years ago
• sdchandra / CNAclinic
  ☆26Updated last year
• PapenfussLab / sv_benchmark
  Comprehensive benchmark of structural variant callers
  ☆48Updated 4 years ago
• bioinfo-pf-curie / TMB
  Tumor Mutational Burden
  ☆63Updated 4 months ago
• mozack / abra
  Assembly Based ReAligner
  ☆74Updated 7 years ago
• broadinstitute / VariantBam
  Filtering and profiling of next-generational sequencing data using region-specific rules
  ☆25Updated 9 years ago
• tommyau / bamclipper
  Remove primer sequence from BAM alignments by soft-clipping
  ☆31Updated 6 years ago
• FoundationMedicineInc / SGZ
  ☆43Updated last year
• ccgd-profile / BreaKmer
  A method to identify structural variation from sequencing data in target regions
  ☆32Updated 5 years ago
• shenlab-sinai / chip-seq_preprocess
  A preprocessing pipeline for ChIP-seq, including alignment, quality control, and visualization.
  ☆27Updated 8 years ago
• ding-lab / MuSiC2
  identifying mutational significance in cancer genomes
  ☆62Updated 3 years ago