Alternatives and similar repositories for hlatyping

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

• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆73Updated last year
• 10XGenomics / supernova
  10x Genomics Linked-Read Diploid De Novo Assembler
  ☆65Updated 6 years ago
• bcgsc / HLAminer
  ⛏ HLA predictions from NGS shotgun data
  ☆55Updated 4 months ago
• ENCODE-DCC / long-read-rna-pipeline
  ENCODE long read RNA-seq pipeline
  ☆51Updated 2 years ago
• a-slide / NanoCount
  EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
  ☆64Updated last year
• 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 4 years ago
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆86Updated 7 years ago
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆98Updated last year
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 11 months ago
• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆142Updated 2 months ago
• tobiasrausch / alfred
  BAM Statistics, Feature Counting and Annotation
  ☆150Updated last week
• mortazavilab / swan_vis
  A Python library to visualize and analyze long-read transcriptomes
  ☆63Updated 5 months ago
• mortazavilab / TranscriptClean
  Correct mismatches, microindels, and noncanonical splice junctions in long reads that have been mapped to the genome
  ☆69Updated last year
• smithlabcode / preseq
  Software for predicting library complexity and genome coverage in high-throughput sequencing.
  ☆88Updated last year
• PapenfussLab / StructuralVariantAnnotation
  R package designed to simplify structural variant analysis
  ☆73Updated 3 years ago
• Clinical-Genomics / BALSAMIC
  Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
  ☆54Updated 2 weeks ago
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆80Updated 8 months ago
• Magdoll / SQANTI2
  SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3
  ☆38Updated 5 years ago
• nf-core / oncoanalyser
  A comprehensive cancer DNA/RNA analysis and reporting pipeline
  ☆89Updated this week
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆116Updated last year
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆52Updated last year
• deepomicslab / SpecHLA
  SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, …
  ☆51Updated 2 weeks ago
• adnaniazi / tailfindr
  An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
  ☆54Updated last year
• tao-bioinfo / gff3sort
  GFF3sort: A Perl Script to sort gff3 files and produce suitable results for tabix tools
  ☆51Updated 5 years ago
• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆47Updated 7 years ago
• nf-core / smrnaseq
  A small-RNA sequencing analysis pipeline
  ☆94Updated 4 months ago
• vplagnol / ExomeDepth
  ExomeDepth R package for the detection of copy number variants in exomes and gene panels using high throughput DNA sequencing data.
  ☆74Updated 3 months ago
• bioinfo-pf-curie / TMB
  Tumor Mutational Burden
  ☆61Updated 2 months ago
• Genotek / ClassifyCNV
  ClassifyCNV: a tool for clinical annotation of copy-number variants
  ☆68Updated 2 years ago
• BioinfoUNIBA / REDItools2
  ☆59Updated 3 months ago