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Count number of fasta sequence $ awk '/^>/ { f = !a[$0]++ } f' aaaa.fa > bbbb.fa #count #fasta #oneliner

Add number in fasta header $ awk '/^>/{$0=$0"_"(++i)}1' infile.fa #fasta #header #add #number #count

Count the contigs length in index fasta file with samtools. $ awk '{s+=$2}END{print s}' scaffolds.fasta.fai #Fasta #Index #Length #Count #Size #Samtools

Get the reads in fastq file: awk '{s++}END{print s/4}' file.fastq #reads #count #ngs #fastq

Count the number of bases in fasta file. grep -v ">" file.fasta | wc | awk '{print $3-$1}' #Fasta #Count #Bases

Count the number of sequences in fastaq file. grep -c '^@' sample1.fq #Fastaq #Count #Number #Grep #Dirty #Oneliner #NGS

To count number of fasta entries, I use: grep -c '^>' mySequences.fasta #Perl #Count #Number #Fasta #Linux #Grep

Count the number of occurrence of pattern in a file using Perl. perl -e '$_ = <>; print scalar ( () = m/needle/g ), "\n"' #Perl #Perloneliner #Count #Occurrence

Count the number of "pattern" occurrence in a file grep -o 'pattern' anc.annots.gff | wc -l #Linux #grep #Count #Number #Occurrence

Count the total number of lines in a file. my $total=@{[<INFILE>]}; #Perl #Count #Number #Total #File

perl -nle '$count += () = /XY[0-9]+/g; END {print $count}' inputfile #Count #Perl #Perloneliner