Illumina paired-end sbRNA-seq pipeline

Nextflow pipeline to process already demultiplexed Illumina paired-end FASTQ files from multiple bacterial samples into a gene $\times$ cell count table.

Processing steps

Per sample:

1. Trim reads to adapters using cutadapt. Reads from sbRNA-seq will be flanked by sequences containing cell barcodes and UMIs, so this step trims any extra sequences either side of these flanking sequences.
2. Extract cell barcodes and UMIs using umitools.
3. Map to genome FASTA using bowtie2.
4. Deduplicate mapped reads using umitools.
5. Count deduplicated reads per gene using featureCounts.
6. Count deduplicated reads per gene per cell using umitools.

Other steps

1. Get FASTQ quality metrics with fastqc.
2. Compile the logs of processing steps into an HTML report with multiqc.

Requirements

Software

You need to have Nextflow and either conda or mamba installed on your system. If possible, use mamba because it will be faster.

Reference genome and genome annotations

You also need the genome FASTA and GFF annotations for the bacteria you are sequencing. These can be obtained from NCBI Nucleotide:

1. Search for your strain of interest, and open its main page
2. On the right-hand side, click Customize view, then Customize and check Show sequence. Finally, click Update view. You may have to wait a few minute while the sequence downloads.
3. Click Send to: > Complete record > File > [FASTA or GFF3] > Create file
4. Save the files to directories which you provide as parameters below.

First time using Nextflow?

If it's your first time using Nextflow on your system, you can install it using conda:

conda install -c bioconda nextflow 

You may need to set the NXF_HOME environment variable. For example,

mkdir -p ~/.nextflow
export NXF_HOME=~/.nextflow

To make this a permanent change, you can do something like the following:

mkdir -p ~/.nextflow
echo "export NXF_HOME=~/.nextflow" >> ~/.bash_profile
source ~/.bash_profile

Quick start

Make a sample sheet (see below) and, optionally, a nextflow.config file in the directory where you want the pipeline to run. Then run Nextflow.

nextflow run scbirlab/nf-sbrnaseq

Each time you run the pipeline after the first time, Nextflow will use a locally-cached version which will not be automatically updated. If you want to ensure that you're using the very latest version of the pipeline, use the -latest flag.

nextflow run scbirlab/nf-sbrnaseq -latest

For help, use nextflow run scbirlab/nf-sbrnaseq --help.

The first time you run the pipeline on your system, the software dependencies in environment.yml will be installed. This may take several minutes.

Inputs

The following parameters are required:

• sample_sheet: path to a CSV containing sample IDs matched with FASTQ filenames, genome information, and adapter sequences.
• fastq_dir: path to directory containing the FASTQ files
• genome_fasta_dir: path to directory containing genome FASTA files (for mapping)
• genome_gff_dir: path to directory containing genome GFF files (for feature counting)

The following parameters have default values can be overridden if necessary.

• trim_qual = 10 : For cutadapt, the minimum Phred score for trimming 3' calls
• min_length = 11 : For cutadapt, the minimum trimmed length of a read. Shorter reads will be discarded
• umitools_error = 6: For umitools, the number of errors allowed to correct cell barcodes
• strand = 1 : For featureCounts, the strandedness of RNA-seq. 1 for forward, 2 for reverse.
• ann_type = 'gene' : For featureCounts, features from GFF column 3 to use for counting
• label = 'Name' : For featureCounts, one or more (comma-separated) fields from column 9 of GFF for labeling counts

The parameters can be provided either in the nextflow.config file or on the nextflow run command.

Here is an example of the nextflow.config file:

params {
   
    sample_sheet = "/path/to/sample_sheet.csv"
    fastq_dir = "/path/to/fastqs"

    genome_fasta_dir = "/path/to/fastas"
    genome_gff_dir = "/path/to/gffs"
}

Alternatively, you can provide these on the command line:

nextflow run scbirlab/nf-sbrnaseq \
    --sample_sheet /path/to/sample_sheet.csv \
    --fastq_dir /path/to/fastqs \
    --genome_fasta_dir /path/to/fastas \
    --genome_gff_dir /path/to/gffs

Sample sheet

The sample sheet is a CSV file providing information about which demultiplexed FASTQ files belong to which sample, which genome each sample should be mapped to, and the UMI and cell barcode scheme for each sample.

The file must have a header with the column names below, and one line per sample to be processed.

• sample_id: the unique name of the sample
• fastq_pattern: the search glob to find FASTQ files for each sample in fastq_dir. The pipleine will look for files matching <fastq_dir>/*<fastq_pattern>*, and should match only two files, corresponding to paired reads.
• genome_id: the name of the genome to map to. Each entry must match the name of one file (apart from the extension) in genome_fasta_dir and genome_gff_dir
• adapter_read1_3prime: the 3' adapter on the forward read to trim to in cutadapt format. The adapter itself and sequences downstream will be removed.
• adapter_read2_3prime: the 3' adapter on the reverse read to trim to in cutadapt format. The adapter itself and sequences downstream will be removed.
• adapter_read1_5prime: the 5' adapter on the forward read to trim to in cutadapt format. Sequences upstream will be removed, but the adapters themselves will be retained.
• adapter_read2_5prime: the 5' adapter on the reverse read to trim to in cutadapt format. Sequences upstream will be removed, but the adapters themselves will be retained.
• umi_read1: the cell barcode and UMI pattern in umitools regex format for the forward read
• umi_read2: the cell barcode and UMI pattern in umitools regex format for the reverse read

Here is an example of the sample sheet:

sample_id	fastq_pattern	genome_id	adapter_read1_3prime	adapter_read2_3prime	adapter_read1_5prime	adapter_read2_5prime	umi_read1	umi_read2
EcoHX1	G5512A22_R	EcoMG1655-NC_000913.3	CAGN{6}G{3};e=1	N{7}N{8}TTATTATA	TATAATAAN{8}N{7}	C{3}N{6}CTG	^(?P<discard_1>.{3})(?P<cell_1>.{6}).*	^(?P<discard_2>.{8})(?P<cell_2>.{8})(?P<umi_1>.{7}).*
EcoHX2	G5512A23_R	EcoMG1655-NC_000913.3	CAGN{6}G{3};e=1	N{7}N{8}TTATTATA	TATAATAAN{8}N{7}	C{3}N{6}CTG	^(?P<discard_1>.{3})(?P<cell_1>.{6}).*	^(?P<discard_2>.{8})(?P<cell_2>.{8})(?P<umi_1>.{7}).*

Outputs

Outputs are saved in the same directory as sample_sheet. They are organised under three directories:

• processed: FASTQ files and logs resulting from trimming and UMI extraction
• counts: tables and BAM files corresponding to cell $\times$ gene counts
• multiqc: HTML report on processing steps

Issues, problems, suggestions

Add to the issue tracker.

Further help

Here are the help pages of the software used by this pipeline.

• fastqc
• multiqc
• nextflow
• cutadapt
• umitools
• featureCounts
• bowtie2
• samtools