Alternatives and similar repositories for bedtk:

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

• PacificBiosciences / barcoding
  Lima - Demultiplex Barcoded PacBio Samples
  ☆65Updated 3 months ago
• milkschen / leviosam2
  Fast and accurate coordinate conversion between assemblies
  ☆112Updated 4 months ago
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆84Updated 6 years ago
• tobiasrausch / alfred
  BAM Statistics, Feature Counting and Annotation
  ☆146Updated 3 months ago
• brentp / duphold
  don't get DUP'ed or DEL'ed by your putative SVs.
  ☆103Updated 4 years ago
• tobiasrausch / wally
  Wally: Visualization of aligned sequencing reads and contigs
  ☆111Updated last month
• cpockrandt / genmap
  GenMap - Fast and Exact Computation of Genome Mappability
  ☆104Updated 7 months ago
• wurmlab / flo
  Same species annotation lift over pipeline.
  ☆96Updated last year
• kcleal / dysgu
  Toolkit for calling structural variants using short or long reads
  ☆100Updated last week
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆92Updated 10 months ago
• epi2me-labs / modbam2bed
  ☆48Updated 5 months ago
• walaj / VariantBam
  Filtering and profiling of next-generational sequencing data using region-specific rules
  ☆74Updated last year
• cortes-ciriano-lab / savana
  Somatic structural variant caller for long-read data
  ☆55Updated this week
• giesselmann / nanopype
  Snakemake pipelines for nanopore sequencing data archiving and processing
  ☆88Updated 2 years ago
• brentp / jigv
  igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"
  ☆126Updated last year
• parklab / bamsnap
  ☆118Updated 2 months ago
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆79Updated 11 months ago
• nanoporetech / wub
  Tools and software library developed by the ONT Applications group
  ☆62Updated 4 years ago
• ENCODE-DCC / long-read-rna-pipeline
  ENCODE long read RNA-seq pipeline
  ☆44Updated 2 years ago
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆67Updated 4 months ago
• smithlabcode / preseq
  Software for predicting library complexity and genome coverage in high-throughput sequencing.
  ☆80Updated 3 months ago
• parklab / xTea
  Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
  ☆103Updated last week
• ryanlayer / stix
  Structural Variant Index
  ☆71Updated last month
• adnaniazi / tailfindr
  An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
  ☆54Updated 3 months ago
• nanoporetech / pinfish
  Tools to annotate genomes using long read transcriptomics data
  ☆45Updated 4 years ago
• svviz / svviz
  Read visualizer for structural variants
  ☆81Updated 6 years ago
• ssadedin / bazam
  A read extraction and realignment tool for next generation sequencing data
  ☆99Updated 2 years ago
• arq5x / bedtools-protocols
  ☆78Updated 10 years ago
• a-slide / NanoCount
  EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
  ☆57Updated 3 months ago
• KolmogorovLab / Severus
  A tool for somatic structural variant calling using long reads
  ☆113Updated last week