Everything about FASTQ format

🧭 Start here: a 6-step reading path

1. Read the overview: FASTQ formatA 5-minute orientation
2. Read the landmark paper: The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variantsCited 1,610 times
3. Go sideways: Phred quality scoreA closely related topic
4. Go sideways: SAM (file format)A closely related topic

🏆 Landmark papers (most cited)

• The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

  Peter J. A. Cock, Christopher J. Fields, Naohisa Goto · 2009 · Nucleic Acids Research · 1,610 citations

• Compression of FASTQ and SAM Format Sequencing Data

  James K. Bonfield, Matthew V. Mahoney · 2013 · PLoS ONE · 184 citations

• Compression of DNA sequence reads in FASTQ format

  Sebastian Deorowicz, Szymon Grabowski · 2011 · Bioinformatics · 131 citations

• The FASTQ+ format and PISA

  Quan Shi, Shiping Liu, Karsten Kristiansen · 2022 · Bioinformatics · 57 citations

• fastQ_brew: module for analysis, preprocessing, and reformatting of FASTQ sequence data

  Damien M. O’Halloran · 2017 · BMC Research Notes · 12 citations

• Parallel Compression and Decompression of DNA Sequence Reads in FASTQ Format

  Jingjing Zheng, Ting Wang · 2014 · International Journal of Hybrid Information Technology · 1 citations

• A Method for Hypermutated Viral Sequences Detection in Fastq and Bam Format Files

  Hamid Alinejad-Rokny, Masoudeh Masoud · 2016 · Journal of Medical Imaging and Health Informatics · 0 citations

📚 Books worth reading

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🔗 Related topics

• Phred quality score A Phred quality score is a measure of the quality of the identification of the nucleobases generated by automated DNA sequencing. It was originally developed…
• SAM (file format) Sequence Alignment Map (SAM) is a text-based format originally for storing biological sequences aligned to a reference sequence developed by Heng Li and…
• BAM (file format) The BAM file format (which stands for Binary Alignment Map) is the lossless, compressed binary representation of a Sequence Alignment Map file. It is compressed…
• Sequence assembly In bioinformatics, sequence assembly refers to aligning and merging fragments from a longer DNA sequence in order to reconstruct the original sequence…
• DNA sequencer A DNA sequencer is a scientific instrument used to automate the process of DNA sequencing. Given a DNA sample, the DNA sequencer is used to determine the…
• Bioconductor Bioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments…
• BED (file format) The BED (Browser Extensible Data) format is a text file format used to store genomic regions as coordinates and associated annotations. The data are presented…
• Pileup format Pileup format is a text-based format for summarizing the base calls of aligned reads to a reference sequence. This format facilitates visual display of…