Table 2.
File types processed during the testing phase of the aws-s3-integrity-check tool.
| File type | Description |
|---|---|
| Bam | Compressed binary version of a SAM file that represents aligned sequences up to 128 Mb. |
| Bed | Browser Extensible Data format. This file format is used to store genomic regions as coordinates. |
| Csv | Comma-Separated Values. |
| Docx | File format for Microsoft Word documents. |
| Fa | File containing information about DNA sequences and other related pieces of scientific information. |
| Fastq | Text-based format for storing genome sequencing data and quality scores. |
| Gct | Gene Cluster Text. This is a tab-delimited text format file that contains gene expression data. |
| Gff | General Feature Format is a file format used for describing genes and other features of DNA, RNA, and protein sequences. |
| Gz | A file compressed by the standard GNU zip (gzip). |
| Html | HyperText Markup Language file. |
| Ibd | Pre-processed mass spectrometry imaging (MSI) data. |
| imzML | Imaging Mass Spectrometry Markup Language. Contains raw MSI data. |
| Ipynb | Computational notebooks that can be opened with Jupyter Notebook. |
| Jpg | Compressed image format for containing digital images. |
| JSON | JavaScript Object Notation. Text-based format to represent structured data based on JavaScript object syntax. |
| md5 | Checksum file. |
| Msa | Multiple sequence alignment file. It generally contains the alignment of three or more biological sequences of similar length. |
| Mtx | Sparse matrix format. This contains genes in the rows and cells in the columns. It is produced as output by Cell Ranger. |
| Npy | Standard binary file format in NumPy [27] for saving numpy arrays. |
| Nwk | Newick tree file format to represent graph-theoretical trees with edge lengths using parentheses and commas. |
| Portable Document Format. | |
| Py | Python file. |
| Pyc | Compiled bytecode file generated by the Python interpreter after a Python script is imported or executed. |
| R | R language script format. |
| Svg | Scalable Vector Graphics. This is a vector file format. |
| Tab | Tab-delimited text or data files. |
| Tif | Tag Image File Format. Tif is a computer file used to store raster graphics and image information. |
| Tsv | Tab-separated values to store text-based tabular data. |
| Txt | Text document file. |
| Vcf | Variant Call Format. Text file for storing gene sequence variations. |
| Xls | Microsoft Excel Binary File format. |
| Zip | A file containing one or more compressed files. |