'wc' is faster than awk

#yourfile.fastq  
echo $(cat yourfile.fastq|wc -l)/4|bc

#yourfile.fastq.gz
 echo $(zcat yourfile.fastq.gz|wc -l)/4|bc

for fasta files: grep -c "^>" file.fasta

for fastq files: grep -c "^@" file.fastq

for fastq files: awk '{s++}END{print s/4}' file.fastq

Here is the fancy script in bash:

#!/bin/bash
if [ $# -lt 1 ] ; then
    echo ""
    echo "usage: count_fastq.sh [fastq_file1] <fastq_file2> ..|| *.fastq"
    echo "counts the number of reads in a fastq file"
    echo ""
    exit 0
fi
 
filear=${@};
for i in ${filear[@]}
do
lines=$(wc -l $i|cut -d " " -f 1)
count=$(($lines / 4))
echo -n -e "\t$i : "
echo "$count"  | \
sed -r '
  :L
  s=([0-9]+)([0-9]{3})=\1,\2=
  t L'
done

Save this as a file (like count_fastq.sh ), then

chmod +x count_fastq.sh

After this you can run it on your file as:

./count_fastq.sh your_file.fastq

for i in `ls *.fastq.gz`; do echo $(zcat ${i} | wc -l)/4|bc; done

• of note: ` are around ls .fastq.gz

Explanation:

For all gzip compressed fastq files, display the number of reads since 4 lines = 1 reads

*Just a good one-liner to see how many reads obtained from something like demultiplexing went

couldn't we just count the number of separations between the sequence and quality score lines?

grep -c "^+$" ./ref.fastq

$readnumber= {(wc-l <name of fastq file>) /4 } *2

LINE_COUNT=$(wc -l filename.fastq)             #Counts the number of lines in fastq file
PART=(${LINE_COUNT//\t/ })                          # Removes the file name from the output and only returns number of lines
READ_COUNT=$((PART[0]/4))                       # Divides the number of lines by 4 which equals the number of reads

A non command line approach for fastq files is to use FastQC, a quality control checking program which is part of many workflows to get a general idea of sequence quality.

Number of reads is listed in the summary statistics at the beginning of the report.

If you're looking at fastq files for the first time, you will probably want to do more than just counting the number of reads, and for that I would recommend downloading FASTQC.

Really good tool for assessing the state of your sequencing data.