Alternatives and similar repositories for sv-callers

Users that are interested in sv-callers are comparing it to the libraries listed below

• tao-bioinfo / gff3sort
  GFF3sort: A Perl Script to sort gff3 files and produce suitable results for tabix tools
  ☆51Updated 5 years ago
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆85Updated 6 years ago
• GeneDx / scramble
  ☆39Updated last year
• a-slide / NanoCount
  EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
  ☆61Updated 9 months ago
• adnaniazi / tailfindr
  An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
  ☆54Updated 9 months ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆50Updated 11 months ago
• nf-core / oncoanalyser
  A comprehensive cancer DNA/RNA analysis and reporting pipeline
  ☆76Updated this week
• mortazavilab / TranscriptClean
  Correct mismatches, microindels, and noncanonical splice junctions in long reads that have been mapped to the genome
  ☆68Updated last year
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆96Updated last year
• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆140Updated last month
• ENCODE-DCC / long-read-rna-pipeline
  ENCODE long read RNA-seq pipeline
  ☆49Updated 2 years ago
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆72Updated 10 months ago
• mskilab-org / JaBbA
  MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.
  ☆57Updated 3 months ago
• deepomicslab / SpecHLA
  SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, …
  ☆46Updated 3 months ago
• pwwang / vcfstats
  Powerful statistics for VCF files
  ☆70Updated last year
• fritzsedlazeck / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆48Updated 5 years ago
• mortazavilab / swan_vis
  A Python library to visualize and analyze long-read transcriptomes
  ☆62Updated 2 months ago
• nf-core / variantbenchmarking
  Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research
  ☆31Updated last week
• hartwigmedical / pipeline5
  ☆21Updated this week
• WGLab / LIQA
  Long-read Isoform Quantification and Analysis
  ☆38Updated 3 months ago
• ygidtu / trackplot
  trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and fu…
  ☆93Updated last month
• SciLifeLab / TIDDIT
  TIDDIT - structural variant calling
  ☆74Updated 3 months ago
• walaj / VariantBam
  Filtering and profiling of next-generational sequencing data using region-specific rules
  ☆78Updated last year
• parklab / ShatterSeek
  ☆69Updated 2 years ago
• PacificBiosciences / barcoding
  Lima - Demultiplex Barcoded PacBio Samples
  ☆67Updated 2 months ago
• wyang17 / SQuIRE
  Software for Quantifying Interspersed Repeat Expression
  ☆60Updated 3 years ago
• tobiasrausch / alfred
  BAM Statistics, Feature Counting and Annotation
  ☆150Updated 3 weeks ago
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 8 months ago
• shimlab / BLAZE
  SingleCell Nanopore sequencing data analysis
  ☆60Updated last month
• tderrien / FEELnc
  FEELnc : FlExible Extraction of LncRNA
  ☆89Updated 10 months ago