7 useful bash shortcuts for bioinformatics

Garth Kong · September 10, 2020

Bash   Bioinformatics

Monitor SLURM jobs in real time

watch squeue -u $(whoami)

Monitor file sizes in real time

watch du -shc *

Monitor files as they are made or edited

watch tree .

List files in long format, organized by time of edit, in human read-able format

ls -lrth
# l = long list format
# r = reverse order
# t = organize by time
# h = memory in human-readable format

Count number of reads in all bam files in a directory

# in parallel
ls *.bam | parallel "echo {} && samtools view -c {}"

# in serial
for i in $(ls *.bam); do echo $i && samtools view -c $i; done

Index all bam files in a directory

for i in $(ls *.bam); do echo "indexing $i" && samtools index -@ 4 -b $i; done

Symlink many files to a directory

for i in $(find /path/of/interest/ -name *.gz | grep "more_filter_terms" | sort); do ln -s $i .; done

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