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The trimmomatic command can be ran with multiple threads, running simply . Run the trimmomatic call from the command-line to see details on the -threads option.
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| Code Block |
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[]$ salloc -A arcc -t 1:00:00 -c 16
[@m001 trimmmomatic] trimmomatic PE -threads 16 \
data/SRR2589044_1.fastq.gz data/SRR2589044_2.fastq.gz \
SRR2589044_1.trim.fastq.gz SRR2589044_1un.trim.fastq.gz \
SRR2589044_2.trim.fastq.gz SRR2589044_2un.trim.fastq.gz \
SLIDINGWINDOW:4:20 MINLEN:25 ILLUMINACLIP:adapters/NexteraPE-PE.fa:2:40:15 |
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Adapters:
Adapters are available at the trimmomatic Git Hub. A batch script would take the following form where we are defining and using 8 cores (on a single node).
On Beartooth, the following adapters are available, and can be copied from: /apps/u/opt/linux/trimmomatic/0.39/adapters/
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