chromsizes

chromSizes is a simple text file that records the sizes of chromosomes for a particular genome assembly. It is a common input for genome browsers and analysis tools to determine chromosome lengths and to set visualization scales and coordinate systems.

Format typically consists of two columns: the chromosome name and its length in base pairs. Columns are usually separated by a tab or whitespace. Many pipelines require no header, though some workflows accommodate a header line such as "chrom" and "size" or "chrom\tsize." The essential content is a straightforward mapping from chromosome identifier to length.

Generation and source commonly involve deriving lengths from a reference genome FASTA or assembly metadata. Tools such as UCSC’s faSize or fetchChromSizes can generate chromSizes files directly from a FASTA, producing a list of chromosome names paired with their respective lengths. The resulting file is platform-independent and easy for software to parse.

Usage spans a range of visualization and analysis tasks. chromSizes is used to initialize genome tracks in viewers, to bound plots, and to define coordinate limits for coordinate-based manipulations. In Hi-C and other chromatin conformation workflows, it helps govern binning strategies and the scaling of contact maps. It can also serve as a lightweight index for tools that operate on per-chromosome data or that convert data between coordinate systems.

Naming and variants vary by community and tool. While chrom.sizes is a widely encountered filename, chromSizes (camel case) is also common. Regardless of naming, the core concept remains a two-column, tab-delimited list of chromosome names and their lengths, essential for accurate genomic visualization and analysis.