This image implements Brian Bushnell's BBTools.
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/.
(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