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lentendu / DeltaMP

A flexible, reproducible and resource efficient metabarcoding amplicon pipeline for HPC
GNU General Public License v3.0
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Issue with ASV and swarm clustering not accepting N's #179

Open lentendu opened 1 year ago

lentendu commented 1 year ago

Need to truncate sequence from first N at Illumina_fastq and trim, then sequences truncated too short will be removed any how at Illumina_quality

seqkit subseq --bed <(seqkit locate --bed -rP -p "^[ATCG][ATCG]*" some.fastq.gz) some.fastq.gz | seqkit stat