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Modern bioinformatics requires the use of many field-specific file formats. Two of the most prevalent formats for representing biological sequences are FASTA (Pearson & Lipman, 1988) and FASTQ (Cock, Fields, Goto, Heuer, & Rice, 2010). While multiple feature-rich Python bioinformatics libraries exist that can process biological sequence files (Cock et al., 2009; scikit-bio Development Team, 2013), they require complex compiled dependencies that may limit their use in non-Unix environments. Other FASTA or FASTQ specific Python libraries (Du, 2019; Hunt, 2013; Pedersen, 2010; Shirley, Ma, Pedersen, & Wheelan, 2015) are outdated, require runtime dependencies, or make heavy use of C extensions that prioritize speed over readability and portability.

fqfa: A pure Python package for genomic sequence files