Alternatives and similar repositories for UMI-tools:

Users that are interested in UMI-tools are comparing it to the libraries listed below

• hbctraining / Intro-to-ChIPseq
  Intro to ChIPseq using HPC
  ☆294Updated 2 years ago
• ENCODE-DCC / atac-seq-pipeline
  ENCODE ATAC-seq pipeline
  ☆402Updated 7 months ago
• sdparekh / zUMIs
  zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
  ☆278Updated 7 months ago
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆697Updated this week
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆335Updated 6 months ago
• shenlab-sinai / ngsplot
  Quick mining and visualization of NGS data by integrating genomic databases
  ☆263Updated last year
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆393Updated last week
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆793Updated 7 months ago
• nservant / HiC-Pro
  HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
  ☆394Updated 10 months ago
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆450Updated 2 months ago
• hbctraining / DGE_workshop
  ☆384Updated 3 years ago
• hbctraining / In-depth-NGS-Data-Analysis-Course
  ☆442Updated 4 years ago
• ENCODE-DCC / chip-seq-pipeline2
  ENCODE ChIP-seq pipeline
  ☆254Updated last year
• broadinstitute / gtex-pipeline
  GTEx & TOPMed data production and analysis pipelines
  ☆357Updated 3 weeks ago
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆288Updated 3 years ago
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆406Updated last month
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆720Updated this week
• 10XGenomics / cellranger
  10x Genomics Single Cell Analysis
  ☆381Updated last week
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆487Updated 3 weeks ago
• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆197Updated last week
• nf-core / chipseq
  ChIP-seq peak-calling, QC and differential analysis pipeline.
  ☆206Updated 3 weeks ago
• saketkc / pysradb
  Package for fetching metadata and downloading data from SRA/ENA/GEO
  ☆321Updated this week
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆380Updated 2 months ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆538Updated 7 months ago
• scRNA-tools / scRNA-tools
  Table of software for the analysis of single-cell RNA-seq data.
  ☆313Updated this week
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆428Updated 11 months ago
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆588Updated 9 months ago
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆269Updated 8 months ago
• nf-core / sarek
  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  ☆423Updated this week
• pyranges / pyranges
  Performant Pythonic GenomicRanges
  ☆453Updated 8 months ago