One line, when multiple are not enough 👍

Give a 2 column, tab separated list of read no. and read length from fastq file

zcat whatever.fastq.gz | paste - - - - | awk '{print NR " " (length($3))}'

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Count total reads in a fastq file

zcat whatever.fastq.gz | wc -l | awk '{print $1/4}'

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Change extension of multiple files at once.

In below example, the extension changes from *.scafSeq to *.fa

for f in *.scafSeq; do mv "$f" "$(basename "$f" .scafSeq).fa"; done

rename command can also come handy in such cases. For e.g. Rename all .fastq files as .fasta

rename .fastq .fasta *.fastq

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Get A T G C counts for all sequences from a multi fasta file

echo -e "seq_id\tA\tU\tG\tC"; while read line; do echo $line | grep ">" | sed 's/>//g'; for i in A U G C;do echo $line | grep -v ">" | grep -o $i | wc -l | grep -v "^0"; done; done < test.fa | paste - - - - -

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Counting number of sequences in a fasta file:

grep -c "^>" file.fa

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Add something to end of all header lines:

sed 's/>.*/&WHATEVERYOUWANT/' file.fa > outfile.fa

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Clean up a fasta file so only first column of the header is outputted:

awk '{print $1}' file.fa > output.fa

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Count the number of sequences in clusters generating using CD-HIT:

for i in *.clstr; do echo $i ; grep ">Cluster" -B 1 $i --no-group-separator | paste - - | awk '{print $1"_"$2 " "$3+1}' > $i.count.txt ; done

Change extension of fastq files in batch

rename 's/_fastp.fastq.gz/.fq.gz/' *.gz