test-datasets porepatrol

Test data to be used for automated testing with the nf-core/porepatrol pipeline.

Content of this repository

nanopore_reads.fastq.gz: Basecalled ONT reads, gzipped.

Dataset origin

This dataset was obtained from:

https://melbourne.figshare.com/articles/Basecalled_ONT_reads/5170843, by Ryan Wick.

The sample is from a bacteria, sequenced with MinION, and basecalled with Albacore.

I downloaded file barcode04.fastq.gz

I subsampled to 0.5% with seqtk:

gunzip barcode04.fastq.gz
seqtk sample barcode04.fastq 0.005 > nanopore_reads.fastq
gzip nanopore_reads.fastq

Expected output

Running the pipeline locally with the default parameters:

nextflow run porepatrol --reads nanopore_reads.fastq.gz 

The number of reads and number of bases are summarized in results/read_summary/read_summary.txt:

Stage	Number of reads	Number of bases
Input	35	629,487
After adapter chop	35	626,738
After filtering	26	465,573