Convert FASTQ to FASTA on the command line

Various tools exist for converting a FASTQ file to FASTA format. However, a simple unix trick usually do the job. No need to download and install any software.

paste - - - - < file.fq | cut -f 1,2 | sed 's/^@/>/' | tr "\t" "\n" > file.fa

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Last updated on May 06, 2013

ecSeq is a bioinformatics solution provider with solid expertise in the analysis of high-throughput sequencing data. We organize public workshops and conduct on-site trainings on NGS data analysis.

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