Alternatives and similar repositories for UMICollapse

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

• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆140Updated 3 weeks ago
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆96Updated last year
• mskilab-org / JaBbA
  MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.
  ☆57Updated 3 months ago
• Kuanhao-Chao / splam
  ✂️ Deep learning-based splice site predictor that improves spliced alignments
  ☆52Updated 4 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…
  ☆66Updated 2 years ago
• ydLiu-HIT / deSALT
  deSALT - De Bruijn graph-based Spliced Aligner for Long Transcriptome reads
  ☆44Updated 2 years ago
• HKU-BAL / ClairS
  ClairS - a deep-learning method for long-read somatic small variant calling
  ☆85Updated 3 weeks ago
• HKU-BAL / ClairS-TO
  ClairS-TO - a deep-learning method for tumor-only somatic variant calling
  ☆62Updated 3 months ago
• KolmogorovLab / Wakhan
  Haplotype-specific somatic copy number aberrations/profiling from long reads sequencing data
  ☆50Updated this week
• huangnengCSU / longcallR
  LongcallR is a SNP caller for single molecule long-read RNA-seq data
  ☆63Updated 3 weeks ago
• biocore-ntnu / epic2
  Ultraperformant reimplementation of SICER
  ☆56Updated 3 years ago
• nanoporetech / pinfish
  Tools to annotate genomes using long read transcriptomics data
  ☆45Updated 4 years ago
• cpockrandt / genmap
  GenMap - Fast and Exact Computation of Genome Mappability
  ☆107Updated last year
• COMBINE-lab / oarfish
  long read RNA-seq quantification
  ☆86Updated 2 weeks ago
• human-pangenomics / hpp_pangenome_resources
  ☆114Updated last year
• epi2me-labs / fastcat
  Simple utility to concatenate .fastq(.gz) files whilst creating a summary of the sequences.
  ☆38Updated 3 months ago
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆80Updated 4 months 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 6 months ago
• ArcInstitute / xsra
  An efficient CLI to extract sequences from the SRA
  ☆105Updated this week
• brentp / rare-disease-wf
  (WIP) best-practices workflow for rare disease
  ☆60Updated 11 months ago
• fulcrumgenomics / fqtk
  Fast FASTQ sample demultiplexing in Rust.
  ☆62Updated last month
• marbl / HG002
  A complete diploid human genome
  ☆121Updated 5 months ago
• marcelm / dnaio
  Efficiently read and write sequencing data from Python
  ☆64Updated last month
• TrinityCTAT / CTAT-LR-fusion
  fusion transcript detection using long reads, leveraging ctat-minimap2 and FusionInspector
  ☆22Updated 4 months ago
• PacificBiosciences / barcoding
  Lima - Demultiplex Barcoded PacBio Samples
  ☆67Updated last month
• parklab / MuSiCal
  A comprehensive toolkit for mutational signature analysis
  ☆38Updated 11 months ago
• gagneurlab / FRASER
  FRASER - Find RAre Splicing Events in RNA-seq
  ☆46Updated 3 weeks ago
• kcleal / dysgu
  Toolkit for calling structural variants using short or long reads
  ☆105Updated last week
• bioinformatics-centre / BayesTyper
  A method for variant graph genotyping based on exact alignment of k-mers
  ☆87Updated 6 years ago
• a-slide / NanoCount
  EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
  ☆61Updated 8 months ago