nf-core/seqinspector
Dedicated QC-only pipeline for sequencing data. The pipeline will run a (potentially large) set of QC tools and can output global and group specific Multiqc reports. The pipeline is targeting core facilities or research groups with larger sequencing throughput.
Introduction
nf-core/seqinspector is a bioinformatics pipeline that that processes raw sequence data (FASTQ) to provide comprehensive quality control. It can perform subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants. The pipeline generates detailed MultiQC reports with flexible output options, ranging from individual sample reports to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments. If provided, nf-core/seqinspector can also parse statistics from an Illumina run folder directory into the final MultiQC reports.
| Tool Type | Tool Name | Tool Description | Compatibility with Data | Dependencies | Default tool |
|---|---|---|---|---|---|
Subsampling | Seqtk | Global subsampling of reads. Only performs subsampling if --sample_size parameter is given. | [RNA, DNA, synthetic] | [N/A] | no |
Indexing, Mapping | Bwamem2 | Align reads to reference | [RNA, DNA] | [N/A] | yes |
Indexing | SAMtools | Index aligned BAM files, create FASTA index | [DNA] | [N/A] | yes |
QC | FastQC | Read QC | [RNA, DNA] | [N/A] | yes |
QC | FastqScreen | Basic contamination detection | [RNA, DNA] | [N/A] | yes |
QC | SeqFu Stats | Sequence statistics | [RNA, DNA] | [N/A] | yes |
QC | Picard collect multiple metrics | Collect multiple QC metrics | [RNA, DNA] | [Bwamem2, SAMtools, --genome] | yes |
Reporting | MultiQC | Present QC for raw reads | [RNA, DNA, synthetic] | [N/A] | yes |
Usage
If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.
First, prepare a samplesheet with your input data that looks as follows:
samplesheet.csv:
sample,fastq_1,fastq_2,rundir,tags
CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
Now, you can run the pipeline using:
nextflow run nf-core/seqinspector \
-profile <docker/singularity/.../institute> \
--input samplesheet.csv \
--outdir <OUTDIR>Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.
For more details and further functionality, please refer to the usage documentation and the parameter documentation.
Pipeline output
To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.
Credits
nf-core/seqinspector was originally written by the Swedish @NationalGenomicsInfrastructure and Clinical Genomics Stockholm.
We thank the following people for their extensive assistance in the development of this pipeline:
Contributions and Support
If you would like to contribute to this pipeline, please see the contributing guidelines.
For further information or help, don’t hesitate to get in touch on the Slack #seqinspector channel (you can join with this invite).
Citations
An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.
You can cite the nf-core publication as follows:
The nf-core framework for community-curated bioinformatics pipelines.
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.