Alternatives and similar repositories for UMI-tools

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

• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆427Updated 3 months ago
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆472Updated 2 months ago
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆726Updated 2 weeks ago
• hbctraining / Intro-to-ChIPseq
  Intro to ChIPseq using HPC
  ☆309Updated 2 years ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆343Updated last year
• broadinstitute / gtex-pipeline
  GTEx & TOPMed data production and analysis pipelines
  ☆376Updated 2 months ago
• ENCODE-DCC / atac-seq-pipeline
  ENCODE ATAC-seq pipeline
  ☆425Updated last year
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆519Updated 4 months ago
• nservant / HiC-Pro
  HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
  ☆414Updated last year
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆313Updated 4 years ago
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆399Updated last week
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆447Updated last year
• hbctraining / DGE_workshop
  ☆392Updated 3 years ago
• sdparekh / zUMIs
  zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
  ☆281Updated last year
• hbctraining / In-depth-NGS-Data-Analysis-Course
  ☆443Updated 5 years ago
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆830Updated last year
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆392Updated this week
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆299Updated 2 years ago
• ENCODE-DCC / chip-seq-pipeline2
  ENCODE ChIP-seq pipeline
  ☆271Updated last year
• nf-core / chipseq
  ChIP-seq peak-calling, QC and differential analysis pipeline.
  ☆218Updated 3 weeks ago
• 10XGenomics / cellranger
  10x Genomics Single Cell Analysis
  ☆425Updated 5 months ago
• pachterlab / sleuth
  Differential analysis of RNA-Seq
  ☆305Updated 2 months ago
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆751Updated last week
• shenlab-sinai / ngsplot
  Quick mining and visualization of NGS data by integrating genomic databases
  ☆267Updated 2 years ago
• nf-core / sarek
  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  ☆466Updated last week
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆544Updated last year
• aidenlab / juicer
  A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
  ☆452Updated 8 months ago
• milaboratory / mixcr
  MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
  ☆367Updated 2 weeks ago
• thelovelab / DESeq2
  Differential expression of RNA-seq data using the Negative Binomial
  ☆403Updated last week
• STAR-Fusion / STAR-Fusion
  STAR-Fusion codebase
  ☆243Updated last month