ConsensusCruncher - Extended Error Suppression

Welcome to the ConsensusCruncher documentation!

ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to amalgamate reads derived from the same DNA template into a consensus sequence.

To learn more about ConsensusCruncher and its applications, see our publication in Nucleic Acids Research.

Contents:

• Quick start guide
• Tutorial
• How it works
• FAQ

Modes

ConsensusCruncher has 2 modes:

• fastq2bam extracts UMIs and aligns FASTQs with BWA to generate BAM files.

  This script extracts molecular barcode tags and removes spacers from unzipped FASTQ files found in the input directory (file names must contain “R1” or “R2”). Barcode extracted FASTQ files are written to the ‘fastq_tag’ directory and are subsequently aligned with BWA mem. Bamfiles are written to the ‘bamfile” directory under the project folder.

• consensus generates single-strand and duplex consensus sequences with ‘Singleton Correction’

  This script amalgamates duplicate reads in bamfiles into single-strand consensus sequences (SSCS), which are subsequently combined into duplex consensus sequences (DCS). Singletons (reads lacking duplicate sequences) are corrected, combined with SSCS to form SSCS + SC, and further collapsed to form DCS + SC. Finally, files containing all unique molecules (a.k.a. no duplicates) are created for SSCS and DCS.

Commands:

• Extract barcodes
• Single-strand consensus sequences (SSCS)
• Singleton Correction
• Duplex consensus sequences (DCS)