Alternatives and similar repositories for megadepth

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

• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆142Updated last month
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆80Updated 7 months ago
• ssadedin / bazam
  A read extraction and realignment tool for next generation sequencing data
  ☆103Updated 2 years ago
• smithlabcode / preseq
  Software for predicting library complexity and genome coverage in high-throughput sequencing.
  ☆88Updated 11 months ago
• adnaniazi / tailfindr
  An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
  ☆54Updated 11 months ago
• a-slide / NanoCount
  EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
  ☆63Updated 11 months ago
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆86Updated 7 years ago
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• AndreasHeger / gat
  Genomic Association Tester
  ☆32Updated 2 years ago
• walaj / VariantBam
  Filtering and profiling of next-generational sequencing data using region-specific rules
  ☆79Updated last year
• refgenie / refgenie
  Reference genome resource manager
  ☆74Updated last year
• s-andrews / BamQC
  Mapped QC analysis program
  ☆44Updated 7 years ago
• mskilab-org / JaBbA
  MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.
  ☆59Updated 6 months ago
• shimlab / BLAZE
  SingleCell Nanopore sequencing data analysis
  ☆61Updated 4 months ago
• ENCODE-DCC / long-read-rna-pipeline
  ENCODE long read RNA-seq pipeline
  ☆50Updated 2 years ago
• Oshlack / Lace
  Building SuperTranscripts: A linear representation of transcriptome data
  ☆67Updated 4 years ago
• ncbi / BAMscale
  BAMscale is a one-step tool for either 1) quantifying and normalizing the coverage of peaks or 2) generated scaled BigWig files for easy …
  ☆72Updated 10 months ago
• vaquerizaslab / tadtool
  TADtool is an interactive tool for the identification of meaningful parameters in TAD-calling algorithms for Hi-C data.
  ☆48Updated 2 years ago
• NBISweden / GUESSmyLT
  An efficient way to guess the library type of your RNA-Seq data.
  ☆32Updated 2 years ago
• fulcrumgenomics / fqtk
  Fast FASTQ sample demultiplexing in Rust.
  ☆65Updated 4 months ago
• mortazavilab / swan_vis
  A Python library to visualize and analyze long-read transcriptomes
  ☆63Updated 5 months ago
• bartongroup / RATS
  Relative Abundance of Transcripts: An R package for the detection of Differential Transcript isoform Usage.
  ☆34Updated 3 years ago
• fakedrtom / SVAFotate
  ☆44Updated last year
• lh3 / ref-gen
  Human reference genome analysis sets
  ☆55Updated 2 years ago
• LHentges / LanceOtron
  ☆29Updated last year
• huangnengCSU / longcallR
  LongcallR is a SNP caller for single molecule long-read RNA-seq data
  ☆67Updated 3 weeks ago
• Clinical-Genomics / fusion-report
  Tool for parsing outputs from fusion detection tools. Part of a nf-core/rnafusion pipeline. Checkout a live demo at https://matq007.githu…
  ☆28Updated 3 months ago
• Clinical-Genomics / BALSAMIC
  Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
  ☆53Updated last week
• EI-CoreBioinformatics / portcullis
  Splice junction analysis and filtering from BAM files
  ☆42Updated 3 years ago
• dantaki / SV2
  Support Vector Structural Variation Genotyper
  ☆58Updated 5 years ago