Introduction

nf-core/fastqrepair is a bioinformatics pipeline that can be used to recover corrupted FASTQ.gz files, drop or fix uncompliant reads, remove unpaired reads, and settles reads that became disordered. It takes a samplesheet with FASTQ/FASTQ.gz files as input (both single-end and paired-end) and produces clean FASTQ files and QC reports.

1. Recover reads from corrupted fastq.gz file (gzrt)
2. Make recovered reads well-formed (wipertools)
3. Re-pair reads (bbmap/repair.sh)
4. Check QC of recovered reads (FastQC)
5. Aggregate and report QC (MultiQC)

Usage

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

sample,fastq_1,fastq_2
mysampleA,sample_R1.fastq.gz,sample_R2.fastq.gz
mysampleB,sample_R3.fq,sample_R4.fq
mysampleC,sample_R5.fq.gz

Each 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/fastqrepair \
   -profile <test/docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR>

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

This pipeline produces clean and well-formed FASTQ files together with short textual reports of the cleaning actions.

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/fastqrepair was designed and written by Tommaso Mazza.

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 #fastqrepair channel (you can join with this invite).

Citations

If you use nf-core/fastqrepair for your analysis, please cite it using the following doi: 10.5281/zenodo.14796348

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.