Fastquorum

<h1> <picture> <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-fastquorum_logo_dark.png"> <img alt="nf-core/fastquorum" src="docs/images/nf-core-fastquorum_logo_light.png"> </picture> </h1>

Introduction

nf-core/fastquorum is a bioinformatics pipeline that implements the pipeline implements the [fgbio Best Practices FASTQ to Consensus Pipeline][fgbio-best-practices-link] to produce consensus reads using unique molecular indexes/barcodes (UMIs). nf-core/fastquorum can produce consensus reads from single or multi UMI reads, and even [Duplex Sequencing][duplex-seq-link] reads.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!

On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the nf-core website.

| Tools | Description | | ------------------------------------------------------------------------------------------------------------------ | ----------------------------------------------------------------------------------------------------------------------------- | | <p align="center"><img title="Fastquorum Workflow (Tools)" src="docs/images/fastquorum_subway.png" width=100%></p> | <p align="center"><img title="Fastquorum Workflow (Description)" src="docs/images/fastquorum_subway.desc.png" width=100%></p> |

1. Read QC (FastQC)
2. Fastq to BAM, extracting UMIs (fgbio FastqToBam)
3. Align (bwa mem), reformat (fgbio ZipperBam), and template-coordinate sort (samtools sort)
4. Group reads by UMI (fgbio GroupReadsByUmi)
5. Call consensus reads
   1. For [Duplex-Sequencing][duplex-seq-link] data
      1. Call duplex consensus reads (fgbio CallDuplexConsensusReads)
      2. Collect duplex sequencing specific metrics (fgbio CollectDuplexSeqMetrics)
   2. For non-Duplex-Sequencing data:
      1. Call molecular consensus reads (fgbio CallMolecularConsensusReads)
6. Align (bwa mem)
7. Filter consensus reads (fgbio FilterConsensusReads)
8. Present QC (MultiQC)

Verified Vendors, Kits, and Assays

[!WARNING] The following Vendors, Kits, and Assays are provided for informational purposes only. No warranty for the accuracy or completeness of the information or parameters is implied.

| Verified | Assay | Company | Strand | Randomness | UMI Location | Read Structure | URL | | -------- | --------------------------------------------------------- | --------------------------- | ------ | ---------- | ---------------- | --------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | No | SureSelect XT HS | Agilent Technologies | Single | Random | | | link | | No | SureSelect XT HS2 (MBC) | Agilent Technologies | Dual | Random | | | link | | No | TruSight Oncology (TSO) | Illumina | Dual | Nonrandom | | | link | | No | xGen dual index UMI Adapters | Integrated DNA Technologies | Single | Random | index1 (i7) | | link | | No | xGen Prism (xGen cfDNA & FFPE DNA Library Prep MC v2 Kit) | Integrated DNA Technologies | Dual | Nonrandom | | | link | | No | NEBNext | New England Biosciences | Single | Random | index1 (i7) | | link | | No | AML MRD | TwinStrand Biosciences | Dual | Random | | | link | | No | Mutagenesis | TwinStrand Biosciences | Dual | Random | | | link | | No | UMI Adapter System | Twist Biosciences | Dual | Random | Inline (R1 & R2) | 5M2S+T 5M2S+T | link