Next-Generation Sequencing 🧬

  • ASCENT    snakemake
    • ASE (alternate splicing events) are identified and quantified using the ASCENT (Alternate SpliCing EveNt Tools) pipeline. This workflow can be used for multi-group multi-contrasts scenarios.
  • ASPEN    snakemake
    • ASPEN or Atac Seq PipEliNe is CCBR's pipeline to calls peaks for ATAC-Seq datasets. It currently accepts paired-end Illumina data and calls peak using MACS2 and Genrich peak callers.
  • CARLISLE snakemake
    • Cut And Run anaLysIS pipeLinE calls peaks using MACS2, SEACR and GoPeaks on spike-in normalized input fastqs.
  • CCBR_circRNA_AmpliconSeq    snakemake
    • This is a snakemake workflow to process circRNA AmpliconSeq datasets generated to study circRNAs in KSHV and human hosts using divergent primers.
  • CHAMPAGNE    nextflow
    • CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline calls ChIPseq peaks using MACS2, GEM, and SICER followed by motif enrichment and other downstream analysis.
  • CHARLIE    snakemake
    • Circrnas in Host And viRuses anaLysis pIpEline detects, annotates and quantifies circRNAs in host + virus references using CIRCExplorer2, CIRI2 and many other tools in parallel.
  • CRUISE    nextflow
    • Crispr scReen seqUencIng analySis pipEline can be used for whole genome CRISPR KO analysis with MaGeck, Bagel and drugZ.
  • DNAnexus
    • This repository provides access to a set of pipelines developed by CCBR members to analyze NGS data on DNAnexus. They allow a user to process raw data starting from FastQ files to reach common endpoints for downstream analysis such as a list of annotated mutations, a set of annotated peaks, or a raw counts matrix for differential expression analysis.
  • DTEG    nextflow
    • Integration of RNA-seq and Ribo-seq to calculate translation efficiency as the number of ribosomes per gene, normalized to transcript abundance.
  • HapFerret
    • HapFerret is an Expectation-Maximization (EM) implementation that is characterized by flexibility and ease of use, notable its use of a natural format for input genotypes and output haplotypes.
  • HERVx    snakemake
    • Human Endogenous Retrovirus expression pipeline, as known as HERVx, is a containerized pipeline to characterize retrotranscriptome. HERVx calculates Human Endogenous Retrovirus (HERV) expression in paired-end RNA-sequencing data.
  • ISOMIR    nextflow
    • Detection and annotation of microRNA isoforms (isomiRs).
  • l2p
    • List-to-pathway, or l2p, is an R package for gene set enrichment analysis that is optimized for speed.
  • METRO    snakemake
    • Mouse nEoanTigen pRedictOr is a pipeline to characterize the effect of a mutation on an amino acid sequences and to predict the binding of peptides to any MHC molecule using netMHCpan.
  • MAAPster
    • MAAPster, also known as MicroArray Analysis Pipeline, is a comprehensive Shiny application and R package that performs transcriptome analysis of human or mouse Affymetrix gene expression data.
  • MOP2    nextflow
    • Estimation of the length of mRNA poly-A tail from Nanopore reads using Tailfindr and Nanopolish PubMed article link
  • RENEE    snakemake
    • Rna sEquencing aNalysis pipElinE or RENEE is an open-source, reproducible, and scalable solution for analyzing RNA-seq data. The pipeline consists of a series of data processing and quality-control steps orchestrated by Snakemake, a flexible and scalable workflow management system, to submit jobs to a cluster or cloud provider.
  • RiboFootPrint
    • Detection of Ribosomal footprints from NGS data.
  • SF_ATAC-seq    snakemake
    • The ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) pipeline typically follows several steps to analyze paired-end sequencing data and identify regions of open chromatin (peaks).
  • SF_biocontainer
    • SF_biocontainer is a github repo with the Docker file used to build containers for CCRSF pipelines.
  • SF_Fastq-QC    snakemake
    • Sequencing Facility Fastq-QC pipeline: No pipe - an abbreviated pipeline that will run Fastqc, Fastq screen and generate MultiQC report.
  • SF_LR_Transcriptome    snakemake
    • Long read transcriptome pipeline for Pacbio and ONT.
  • SF_LR_VAP    snakemake
    • The SF Long Read Variant Analysis Pipeline (SF_LR_VAP) is a bioinformatics workflow tailored for the comprehensive analysis of long-read sequencing data.
  • SF_Polylox-BC    snakemake
    • This repository contains workflows/scripts for processing Pacbio reads integrated with cell barcodes to Polylox barcodes, generating comprehensive reports and visualizations for Polylox barcode analysis.
  • SINCLAIR    nextflow
    • SINgle CelL AnalysIs Resource or SINCLAIR is developed by the CCR Collaborative Bioinformatics Resource as an open-source, reproducible solution for multiple single cell next-generation modalities.
  • TRANQUIL    snakemake
    • TRANQUIL or "TRna AbundaNce QUantification pIpeLine" is a Snakemake pipeline which quantifies tRNA using the mim-tRNAseq tool.
  • LOGAN    nextflow
    • LOGAN is a comprehensive whole genome-sequencing pipeline following the Broad's set of best practices.
  • XAVIER    snakemake
    • eXome Analysis and VarIant explorER aims to accurately call germline and somatic variants, to infer CNVs, and annotate variants.