HTSeq is a Python library designed to facilitate the rapid development of scripts for processing and analyzing high-throughput sequencing (HTS) data. It offers parsers for common data formats such as FASTA, FASTQ, SAM/BAM, GFF/GTF, VCF, BED, and Wiggle. The library includes classes to represent various data types, including genomic coordinates, sequences, reads, alignments, gene models, and variant calls. A key feature is the GenomicArray class, which efficiently stores and retrieves data associated with genomic positions or intervals. HTSeq also provides tools like `htseq-qa` for read quality assessment and `htseq-count` for preprocessing RNA-Seq data for differential expression analysis. The package is released under the GNU General Public License and is available from the Python Package Index. HTSeq aims to bridge the gap between specialized tools and the need for custom scripts, offering a comprehensive solution for a wide range of HTS data analysis tasks.HTSeq is a Python library designed to facilitate the rapid development of scripts for processing and analyzing high-throughput sequencing (HTS) data. It offers parsers for common data formats such as FASTA, FASTQ, SAM/BAM, GFF/GTF, VCF, BED, and Wiggle. The library includes classes to represent various data types, including genomic coordinates, sequences, reads, alignments, gene models, and variant calls. A key feature is the GenomicArray class, which efficiently stores and retrieves data associated with genomic positions or intervals. HTSeq also provides tools like `htseq-qa` for read quality assessment and `htseq-count` for preprocessing RNA-Seq data for differential expression analysis. The package is released under the GNU General Public License and is available from the Python Package Index. HTSeq aims to bridge the gap between specialized tools and the need for custom scripts, offering a comprehensive solution for a wide range of HTS data analysis tasks.