Spriggan is a NextFlow pipeline used for assembly of bacterial whole genome sequence data and identification of antibiotic resistance genes.
Usage
Workflow outline
Read trimming and quality assessment
Genome assembly
Assembly quality assessment
Genome coverage
Antimicrobial resistance gene detection
MLST scheme
Contamination detection
Output
The pipeline is designed to start from raw Illumina reads. All reads must be in the same directory. Then start the pipeline using:
nextflow sprriggan.nf --reads [path-to-reads]
You can also test the pipeline with example data using --test, note this requires NextFlow version 21.07.0-edge or greater:
nextflow sprriggan.nf --test
You can specify a version of the pipeline and run it directly from the github repository by using:
nextflow wslh-bio/spriggan -r <version> --reads [path-to-reads]
Read trimming and cleaning is performed using BBtools v38.76 to trim reads of low quality bases and remove PhiX contamination. Then FastQC v0.11.8 is used assess the quality of the raw and cleaned reads.
Assembly of the cleaned and trimmed reads is performed using Shovill v1.1.0.
Quality assessment of the assemblies is performed using QUAST v5.0.2
Mean and median genome coverage is determined by mapping the cleaned reads back their the assembly using BWA v0.7.17-r1188 and calculating depth using samtools v1.10
Antimicrobial resistance genes, as well as point mutations, are identified using AMRFinderPlus v3.1.1. Spriggan can generate a table of AMRFinderPlus results for AR genes of interest with the selected_genes parameter. Spriggan will search for matches to the AR genes of interest in the AMRFinderPlus results and make a table called 'selected_ar_genes.tsv.' The list of genes must be separated by | and enclosed in single quotes in the config file. By default the selected_genes parameter is set to: 'NDM|OXA|KPC|IMP|VIM'
MLST scheme is classified using MLST v2.17.6. Multiple schemes are available for specific organisms, and STs from all available schemes are reported for those organisms.
Contamination is detected by classifying reads using Kraken2 v2.0.8 with the Minikraken2_v1_8GB database.
spriggan_results
├── alignments
│ ├── *.(sorted).bam(.bai)
│ ├── *.sam
│ └── *.txt
├── amrfinder
│ ├── ar_predictions.tsv
│ ├── ar_summary.tsv
│ ├── *.amr.tsv
│ └── selected_ar_genes.tsv
├── assembled
│ └── *.contigs.fa
├── coverage
│ ├── coverage_stats.tsv
│ └── *.depth.tsv
├── fastqc
│ ├── fastqc_summary.tsv
│ ├── *.html
│ └── zips
│ └── *.zip
├── kraken
│ ├── kraken_results.tsv
│ └── *.kraken2.txt
├── mlst
│ ├── mlst_results.tsv
│ └── *.mlst.tsv
├── quast
│ ├── quast_results.tsv
│ └── *.quast.tsv
├── multiqc_report.html
├── spriggan_report.csv
└── trimming
├── bbduk_results.tsv
└── *.trim.txt
*.(sorted).bam(.bai) - Alignments in BAM format (sorted and unsorted; includes *.bai index files)
*.sam - Alignments in SAM format
*.txt - Samtools stats output
ar_predictions.tsv - Long-format table of AMRFinderPlus results
ar_summary.tsv - Wide-format table of AMRFinderPlus results
*.amr.tsv - Raw AMRFinderPlus output for each sample
selected_ar_genes.tsv - Table of AMRFinderPlus results for genes selected by user
*.contigs.fa - Shovill assembly for each sample
coverage_stats.tsv - Summary table of mean and median coverage calculated with Samtools depth
*.depth.tsv - Raw Samtools depth output for each sample
fastqc_summary.tsv - Summary table of FastQC results
*.html - HTML files of FastQC results
*.zip - Zipped folders of FastQC output
kraken_results.tsv - Summary table of Kraken results
*.kraken2.txt - Report of Kraken results for each sample
mlst_results.tsv - Summary table of MLST results
*.mlst.tsv - Raw MLST output for each sample
quast_results.tsv - Summary table of QUAST results
*.quast.tsv - QUAST results for each sample
multiqc_report.html - HTML report generated by MultiQC
spriggan_report.csv - Summary table of each step in Spriggan
bbduk_results.tsv - Summary table of trimming with BBDuk
*.trim.txt - Trimming results from BBduk each sample
Kelsey Florek, WSLH Senior Genomics and Data Scientist
Abigail Shockey, WSLH Bioinformatics and Data Scientist