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BBTools

This image implements Brian Bushnell's BBTools.

Includes

To see all of the executables in this image, run the following command inside a container:

ls /usr/local/bin

Documentation is in the /opt/bbmap/docs/ directory, and in each tool's shell script in /opt/bbmap/.

Example Usage

(adapted from /opt/bbmap/pipelines/covid/processCorona.sh)

Interleave a pair of FASTQ files for downstream processing:

reformat.sh \
    in1=${SAMPLE}_R1.fastq.gz \
    in2=${SAMPLE}_R2.fastq.gz \
    out=${SAMPLE}.fastq.gz

Split into SARS-CoV-2 and non-SARS-CoV-2 reads:

bbduk.sh ow -Xmx1g \
    in=${SAMPLE}.fq.gz \
    ref=REFERENCE.fasta \
    outm=${SAMPLE}_viral.fq.gz \
    outu=${SAMPLE}_nonviral.fq.gz \
    k=25