Next-Generation Sequencing 🧬

• ASCENT    
  • 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    
  • 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
  • Cut And Run anaLysIS pipeLinE calls peaks using MACS2, SEACR and GoPeaks on spike-in normalized input fastqs.
• CCBR_circRNA_AmpliconSeq    
  • This is a snakemake workflow to process circRNA AmpliconSeq datasets generated to study circRNAs in KSHV and human hosts using divergent primers.
• CHAMPAGNE    
  • CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline calls ChIPseq peaks using MACS2, GEM, and SICER followed by motif enrichment and other downstream analysis.
• CHARLIE    
  • 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    
  • 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    
  • 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    
  • 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    
  • Detection and annotation of microRNA isoforms (isomiRs).
• iCLIP    
  • Individual-nucleotide resolution Cross-Linking and ImmunoPrecipitation (iCLIP); multi-sample peak identification and annotation analysis; differential analysis using DIFFBIND and MANORM.
• l2p
  • List-to-pathway, or l2p, is an R package for gene set enrichment analysis that is optimized for speed.
• METRO    
  • 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.
• MAPLE    
  • MNase-seq Analysis PipeLinE (MAPLE): multi-sample DYAD fragment identification and quantification.
• MOP2    
  • Estimation of the length of mRNA poly-A tail from Nanopore reads using Tailfindr and Nanopolish PubMed article link
• RENEE    
  • 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    
  • 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    
  • Sequencing Facility Fastq-QC pipeline: No pipe - an abbreviated pipeline that will run Fastqc, Fastq screen and generate MultiQC report.
• SF_LR_SOMATIC    
  • This pipeline processes long-read (LR) sequencing data to identify somatic mutations including single nucleotide variants (SNVs), structural variants (SVs), and copy number alterations (CNAs) using various bioinformatics tools.
• SF_LR_Transcriptome    
  • Long read transcriptome pipeline for Pacbio and ONT.
• SF_LR_VAP    
  • 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_MAS-SC    
  • In the SF Multiplexed Arrays Sequencing (SF_MAS-SC) workflow, full-length cDNA sequences are processed and classified against a reference annotation database. This workflow identifies novel genes and isoforms, and outputs count matrices at both the gene and isoform levels.
• SF_miRNA    
  • This repository contains workflows/scripts for processing small RNA sequencing data. The pipeline includes steps for mapping reads to the reference genome and the miRNA database and estimating the abundance of miRNAs.
• SF_Polylox-BC    
  • 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    
  • 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    
  • TRANQUIL or "TRna AbundaNce QUantification pIpeLine" is a Snakemake pipeline which quantifies tRNA using the mim-tRNAseq tool.
• LOGAN    
  • LOGAN is a comprehensive whole genome-sequencing pipeline following the Broad's set of best practices.
• XAVIER    
  • eXome Analysis and VarIant explorER aims to accurately call germline and somatic variants, to infer CNVs, and annotate variants.