BOL

#Convert #FASTQ to FASTA and set bases of #quality lower than 20 to N $ seqtk seq -aQ64 -q20 -n N IN.fastq > OUT.fasta

fastq-pair: Match up paired end fastq files quickly and efficiently https://github.com/linsalrob/fastq-pair #fastq-pair #fastq

interleave fastq files https://gist.github.com/nathanhaigh/4544979 #interleave #fastq #pair #ngs #reads

Convert interleaved to separate files with BBmap. $ reformat.sh in=reads.fq out1=reads_r1.fq out2=reads_r2.fq #interleave #fastq #seperate #reformat #bbmap

Fastq 2 fasta. $ sed -n '1~4s/^@/>/p;2~4p' test.fastq > test.fasta #fastq #fasta #convert

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

fastq to fasta convertor $ sed -n '1~4s/^@/>/p;2~4p' test.fastq > test.fasta #Convert #Fasta #Fastq #fa #fq