Workflow single-cell

wf-single-cell is a research pipeline designed to identify the cell barcode and UMI sequences present in nanopore sequencing reads generated from single-cell gene expression libraries.

It was initially created as a Nextflow port of Sockeye.

Introduction

The following single-cell kits from 10x Genomics are currently supported:

• Chromium Single Cell 3ʹ gene expression, versions 2 and 3
• Chromium Single Cell 5ʹ gene expression, version 1
• Chromium Single Cell Multiome (ATAC + GEX), version 1

Oxford Nanopore has developed a protocol for sequencing single-cell libraries from 10x, which can be found on the Nanopore Community website.

The inputs to Sockeye are raw nanopore reads (FASTQ) generated from the sequencing instrument and reference files that can be downloaded from 10x. The pipeline outputs gene x cell, and transcript x cell expression matrices, as well as a BAM file of aligned reads tagged with cell barcode and UMI information.

The BLAZE preprint provided useful benchmarking of the original sockeye implementation. This assisted in the selection of appropriate parameters for cell cut-off thresholds and for defining the limits of the cell x gene matrix.

The isoform selection procedure used in this workflow was adapted from that found in the FLAMES package.

Quickstart

The workflow uses nextflow to manage compute and software resources, as such nextflow will need to be installed before attempting to run the workflow.

The workflow can currently be run using either Docker or singularity to provide isolation of the required software. Both methods are automated out-of-the-box provided either docker or singularity is installed.

It is not required to clone or download the git repository in order to run the workflow. For more information on running EPI2ME Labs workflows visit out website.

Workflow options

To obtain the workflow, having installed nextflow, users can run:

nextflow run epi2me-labs/wf-single-cell --help

to see the options for the workflow.

The main options are:

• fastq: A fastq file or directory containing fastq input files or directories of input files.

• ref_genome_dir The path to the 10x reference genome directory (see Downloading reference data below)

• 10x sample metadata using either:

  • The following parameters, which are applied to all samples (the default):
    • kit_name
      • options: 3prime (default), 5prime, multiome
    • kit_version
      • 3prime options: v2, v3 (default)
      • 5prime options: v1
      • multiome options: v1
    • expected_cells [500]

• plot_umaps: This flag controls whether UMAP projections are generated and dispalyed in the report (default false). If UMAP output is required apply like: --plot_umaps.

  or

  • single_cell_sample_sheet (not to be confused with the optional MinKNOW sample_sheet) allowing per sample configuration.

The single_cell_sample_sheet contains details about the input sample_ids, the 10X kits used (e.g. 3prime or 5prime), the kit versions used (v2 or v3 for the 3' kit, v1 for the 5' kit), a rough estimate of the number of cells in the library. The cell count estimate specified with exp_cells and can be a very rough estimate (500 is a robust default value if the number is not known).

The sample_id field should correspond to sample_id which is defined either in the sample_sheet, given by the sample parameter (for single sample runs). If no sample_sheet or sample is given, sample_id is derived from each folder containing the fastq files or if a single file is given, the sample_id is the basename of the file (data.fastq.gz -> data.fastq).

An example sheet with one sample is:

sample_id,kit_name,kit_version,exp_cells
sample_10,3prime,v3,500

Downloading reference data The pipeline requires access to reference data files that are packaged and freely available from 10x Genomics. For human samples, the GRCh38 packaged reference files can be downloaded using either curl or wget using:

curl -O https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2020-A.tar.gz
tar -xvf refdata-gex-GRCh38-2020-A.tar.gz

or

wget https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2020-A.tar.gz
tar -xvf refdata-gex-GRCh38-2020-A.tar.gz

Download demonstration data

A dataset of around 500 MB is provided for the purposes of testing the workflow. It consists of a downsampled dataset of reads mapping to human chromosome 17. The biological sources of the data are five cancer cell lines (see this article) , which can be visualied as clusters in the resulting UMAP plots. It can be downloaded using:

wget https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-single-cell/wf-single-cell-demo.tar.gz \
  && tar -xzvf wf-single-cell-demo.tar.gz

The workflow can be run with the demonstration data using:

OUTPUT=output
nextflow run epi2me-labs/wf-single-cell \
    -w ${OUTPUT}/workspace \
    -profile standard \
    --fastq wf-single-cell-demo/chr17.fq.gz \
    --kit_name 3prime \
    --kit_version v3 \
    --expected_cells 100 \
    --ref_genome_dir wf-single-cell-demo/ \
    --out_dir ${OUTPUT} \
    --plot_umaps

The output of the pipeline will be found in ./output for the above example.

Workflow outputs

The pipeline output will be written to a directory defined by --out_dir. For each sample specifed in the single_cell-sample_sheet an output folder is created containing the results.

The most useful outputs of the pipeline are likely:

• configs.stats.json: provides a summary of sequencing statistics and observed read configurations, such as

  • n_reads: number of total reads in the input fastq(s)
  • rl_mean: mean read length
  • n_fl: total number of reads with the read1-->TSO or TSO'-->read1' adapter configuration (i.e. full-length reads)
  • n_plus: number of reads with the read1-->TSO configuration
  • n_minus: number of reads with the TSO'-->read1' configuration

• bams: Folder of bam alignment files where each alignment contains the following sequence tags

  • CB: corrected cell barcode sequence
  • CR: uncorrected cell barcode sequence
  • CY: Phred quality scores of the uncorrected cell barcode sequence
  • UB: corrected UMI sequence
  • UR: uncorrected UMI sequence
  • UY: Phred quality scores of the uncorrected UMI sequence

  The bam files are output per chromosome (default) unless --merge_bam is set.

• gene_expression.processed.tsv: TSV containing the gene (rows) x cell (columns) expression matrix, processed and normalized according to:

• matrix_min_genes: cells with fewer than this number of expressed genes will be removed
• matrix_min_cells: genes present in fewer than this number of cells will be removed
• matrix_max_mito: cells with more than this percentage of counts belonging to mitochondrial genes will be removed
• matrix_norm_count: normalize all cells to this number of total counts per cell

• transcript_matrix_processed.tsv: TSV containing the transcript (rows) x cell (columns) expression matrix, processed and normalized in the same manner as the genes. These expression values are determined by first generating a transcriptome per sample using stringtie and then assigning reads to transcripts aligning them to this transcriptome with minimap2. Only reads that map unambiguously to a reference transcript are assigned. The assembled transcripts with the following gffcompare class codes are excluded: i, p, s or u. See the gffcompare and this image, and only cells and genes that pass the gene filtering described above are included.
• read_tags.tsv: TSV file witjh the following columns:
  • read_id
  • gene (assigned gene)
  • transcript (assigned transcript id)
  • barcode (corrected barcode)
  • umi )corrected umi

Useful links

• nextflow
• docker
• singularity