Alternatives and similar repositories for uditas

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

• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆80Updated 9 months ago
• mortazavilab / TranscriptClean
  Correct mismatches, microindels, and noncanonical splice junctions in long reads that have been mapped to the genome
  ☆70Updated last year
• a-slide / NanoCount
  EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
  ☆64Updated last year
• walaj / VariantBam
  Filtering and profiling of next-generational sequencing data using region-specific rules
  ☆79Updated 2 years ago
• tao-bioinfo / gff3sort
  GFF3sort: A Perl Script to sort gff3 files and produce suitable results for tabix tools
  ☆51Updated 5 years ago
• ENCODE-DCC / long-read-rna-pipeline
  ENCODE long read RNA-seq pipeline
  ☆51Updated 2 years ago
• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆142Updated 3 months ago
• svviz / svviz
  Read visualizer for structural variants
  ☆84Updated 7 years ago
• CshlSiepelLab / phast
  PHAST
  ☆77Updated last week
• fritzsedlazeck / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆48Updated 5 years ago
• ksahlin / ultra
  Long-read splice alignment with high accuracy
  ☆63Updated last year
• dnanexus-archive / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆103Updated 5 years ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆117Updated last year
• PacificBiosciences / barcoding
  Lima - Demultiplex Barcoded PacBio Samples
  ☆67Updated 6 months ago
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆99Updated last year
• adamewing / tebreak
  Find and characterise transposable element insertions
  ☆20Updated 2 years ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆98Updated 3 years ago
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆75Updated last year
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆86Updated 7 years ago
• mskilab-org / JaBbA
  MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.
  ☆59Updated 8 months ago
• mcfrith / last-rna
  ☆49Updated 2 years ago
• fakedrtom / SVAFotate
  ☆44Updated last year
• AmpliconSuite / CoRAL
  Reconstruction of focal amplifications with long reads
  ☆22Updated 3 weeks ago
• nanoporetech / pipeline-pinfish-analysis
  Pipeline for annotating genomes using long read transcriptomics data with pinfish
  ☆28Updated 4 years ago
• ucdavis-bioinformatics / proc10xG
  processing 10x genomics reads
  ☆26Updated 6 years ago
• bcgsc / HLAminer
  ⛏ HLA predictions from NGS shotgun data
  ☆55Updated 5 months ago
• AndreasHeger / gat
  Genomic Association Tester
  ☆34Updated 2 years ago
• kcleal / dysgu
  Toolkit for calling structural variants using short or long reads
  ☆111Updated 2 months ago
• zhqingit / giremi
  GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data.
  ☆44Updated 8 years ago
• Magdoll / SQANTI2
  SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3
  ☆38Updated 5 years ago