Alternatives and similar repositories for megadepth

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

• smithlabcode / preseq
  Software for predicting library complexity and genome coverage in high-throughput sequencing.
  ☆87Updated 8 months ago
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆85Updated 6 years ago
• adnaniazi / tailfindr
  An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
  ☆54Updated 9 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
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆80Updated 5 months ago
• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆140Updated last month
• a-slide / NanoCount
  EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
  ☆61Updated 9 months ago
• ssadedin / bazam
  A read extraction and realignment tool for next generation sequencing data
  ☆100Updated 2 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 …
  ☆69Updated 7 months ago
• biocore-ntnu / epic2
  Ultraperformant reimplementation of SICER
  ☆56Updated 3 years ago
• drostlab / myTAI
  Evolutionary Transcriptomics with R
  ☆44Updated last week
• Oshlack / Lace
  Building SuperTranscripts: A linear representation of transcriptome data
  ☆67Updated 4 years ago
• tao-bioinfo / gff3sort
  GFF3sort: A Perl Script to sort gff3 files and produce suitable results for tabix tools
  ☆51Updated 5 years ago
• nf-core / oncoanalyser
  A comprehensive cancer DNA/RNA analysis and reporting pipeline
  ☆76Updated this week
• fulcrumgenomics / fqtk
  Fast FASTQ sample demultiplexing in Rust.
  ☆63Updated last month
• mortazavilab / swan_vis
  A Python library to visualize and analyze long-read transcriptomes
  ☆62Updated 2 months ago
• tk2 / RetroSeq
  RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference…
  ☆67Updated 2 years ago
• PapenfussLab / StructuralVariantAnnotation
  R package designed to simplify structural variant analysis
  ☆73Updated 3 years ago
• shimlab / BLAZE
  SingleCell Nanopore sequencing data analysis
  ☆60Updated last month
• AndreasHeger / gat
  Genomic Association Tester
  ☆31Updated 2 years ago
• brentp / jigv
  igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"
  ☆127Updated 2 years ago
• relipmoc / skewer
  ☆95Updated 2 years ago
• jsh58 / NGmerge
  Merging paired-end reads and removing adapters
  ☆44Updated 4 months ago
• refgenie / refgenie
  Reference genome resource manager
  ☆76Updated last year
• brentp / rare-disease-wf
  (WIP) best-practices workflow for rare disease
  ☆60Updated last year
• zd1 / telseq
  A software for calculating telomere length
  ☆70Updated 6 years ago
• nf-core / isoseq
  Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed …
  ☆44Updated last week
• Kingsford-Group / scallop
  Scallop is a reference-based transcriptome assembler for RNA-seq
  ☆92Updated 4 years ago
• smithlabcode / dnmtools
  Tools for analyzing DNA methylation data
  ☆42Updated last week
• bartongroup / RATS
  Relative Abundance of Transcripts: An R package for the detection of Differential Transcript isoform Usage.
  ☆34Updated 3 years ago