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ampliseq is designed for paired-end Illumina data, but can be run on single-end pacbio data with a few modifications:
Manifest file
| Code Block |
|---|
ls *.fastq.gz > read1
cat read1 | sed 's/.fastq.gz//' > ID
paste ID read1 read2 | awk '{print $1 "\t" "/home/whatmorp/nextflow/pacbio_test/fastq/" $2}' > manifest.txt |
A paired-end manifest requires exactly ‘sampleID forwardReads reverseReads’ as column names.
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