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# NextITS pipeline usage examples
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## Quick Start
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``` bash
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nextflow run vmikk/NextITS -r main \
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-profile singularity \
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-resume \
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--step "Step1" \
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--input "pacbio_ccs.fastq.gz" \
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--barcodes "sample_barcodes.fasta" \
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--primer_forward "GTACACACCGCCCGTCG" \
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--primer_reverse "CCTSCSCTTANTDATATGC" \
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--its_region "full" \
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--blast_taxdb "false" \
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--outdir "Results"
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```
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For more examples, see the dedicated [Quickstart section](quickstart.md).
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## Input data
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### Sequences

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