summary_table

• Reads the input stream (single ended fastq) and reports the most frequent DNA fragments.
• usable for QC of barcodes (sample barcodes, cellular barcode) in scRNA-seq
• compiled with gcc >= 4.8.5
• test usage:

gunzip -c data/test.R3.fq.gz | summary_table > data/test.R3.table.csv 2> messages.txt
head data/file.R3.table.csv
cat messages.txt

• real usage:

gunzip -c real_huge.R3.fq.gz | head -n 40000000 | summary_table > real_huge.R3.table.csv 2> messages.txt
cat messages.txt
head real_huge.R3.table.csv

• O2 usage:

sbatch summary_table.sh real_huge.R3.fq.gz

• compilation: compile.sh summary_table.cpp. Result is summary_table binary.